Another consideration is whether you can stick with a single Quantum reactor anyway? There's some zig-zag in the size optimal power solution depending on the actual power requirements. I don't have the numbers in front of me right now, but as I recall, the power requirement of my designs tend to push past 120 around size 300'ish. That said, this consideration really is secondary to me. I'd go with fuel efficiency in the reactor even if it isn't size optimal.
It's true that the optimal number of reactors and which type uses less space is somewhat design dependent. However, the break points really aren't all that favorable to fusion reactors; assuming Fusion 1 and Quantum 1 reactors, a design needs to require less than 84 power to use 1 Fusion instead of 1 Quantum Reactor (saving 3 size), 121-168 power in order to use 2 Fusion instead of 2 Quantum Reactors (a savings of 6 size), 241-252 power to use 3 Fusion instead of 3 Quantum Reactors (saving 9 size, but losing 9 as opposed to just cutting maybe 12 power from the power budget so you can use 2 Quantum Reactors instead of 3 Quantum or 3 Fusion Reactors), and I don't think there's a point beyond that where Fusion Reactors are actually better as far as size requirements go. I can't think of any warship design I have ever made that requires less than 84 power unless it was a prewarp design, and I can't think of that many that require 121-168 power, and there's very little point in hitting the 241-252 power range since it's basically just a blaster or a torpedo either way and you'll have missed the window.
Beyond that, the range isn't greatly improved with Fusion Reactors instead of Quantum Reactors, especially if we're just looking at the first set. 65 fuel (unupgraded standard fuel cells) will provide ~18,700 energy for a Quantum Reactor 1 or ~22,500 energy for a Fusion Reactor 1; assuming a static requirement of 10 and a fully powered Equinox Jumpdrive 1, that's ~4.3e6 range units (~2.15 sectors) per fuel cell with a Fusion Reactor 1 or ~3.6e6 range units (~1.8 sectors) per fuel cell with a Quantum Reactor 1, which means you're only really buying an extra ~0.1 sectors of effective operating range per fuel cell by using Fusion Reactor 1s instead of Quantum Reactor 1s. If we upgrade to Fusion Reactor IIs and Quantum Reactor IIs, the Quantum Reactor ships keep more or less their initial range while the Fusion Reactors go to ~4.5e6 range units (~2.25 sectors) per fuel cell (again assuming a ship with a fully powered Equinox Jumpdrive I and a static requirement of 10) for a whole ~0.15*n sectors of effective operating range more than what the Quantum Reactor ships have with both ship designs carrying n fuel cells. Sorry, but I don't find that to be terribly impressive; that's maybe an extra fuel cell on the ship with Quantum Reactors to make up the range difference when the design with Fusion Reactors carries 10 fuel cells. 650 fuel per ship or 715 fuel per ship is not going to make or break the fuel situation under normal circumstances.
I guess I don't need 3 sector's worth of fuel for simple system defense.
I would not reduce your ships below 3 small fuel cells; assuming the ships are continually at sprint speed and firing constantly during an engagement, the design you posted has no more than 418 real-world seconds of combat time at normal game speed on those ships. That really isn't that much, and the lower the fuel capacities of the ships are, the more frequently they need to stop whatever they're doing to go refuel, increasing the downtime of the defense fleets, thereby increasing the size of the fleet you need to guarantee some certain nominal defensive strength in the region at any given time. Even my short-range ships have at least 5 fuel cells unless I'm really desperate to squeeze something in.
Drop ... energy collectors
I personally would not drop both energy collectors. I'd drop one of them, but if you drop both you're going to see the downtime required for refueling your defense fleets spike sharply, especially if the system in which they're stationed lacks a fuel source (meaning that the fleet has to go somewhere else to refuel). At normal game speed, a ship with 3 small fuel cells, basic space reactors, and a static requirement of 13 will need to refuel roughly once every hour of real time if it lacks energy collectors, even if the only thing the ship does in that time is idle. Adding just one energy collector to that ship will increase its time on station significantly, as it will only burn fuel in combat, immediately before/after combat, and during refueling maneuvers. Size-300 ships are big enough that carrying an energy collector isn't that much of a sacrifice.
I disagree. Early missiles are crap the moment you have to punch through more than a token amount of armor plates and investing research into missile tech upgrades is a bit of a dead end, IMO. If one wants to play the long range game, and I don't see why a min-maxer wouldn't, then velo shards aren't too far away and they're a much better long range weapon that actually lead to an end game worthy upgrade.
The first upgrade of the Concussion Missile keeps it viable, though not great, in the mid-game; that's one tier 1 and one tier 3 tech and 0 refits for a viable, though not great, early mid-game long-range warship upgraded from an early-game long-range warship. Compare that to basing your long-range ships on torpedoes - you need a tier 1 tech, a tier 2 tech, a tier 3 tech, and a refit to keep torpedo designs viable.
Beyond that, at standoff ranges torpedoes really aren't all that much better than missiles against armor, despite the 50% anti-armor penalty suffered by missiles. A Velocity Shard I engaging at 600 range is dealing only 4 damage per shot to a Concussion Missile II's 8 (4 versus armor); Velocity Shard IIs are at 8 damage per shot to the Concussion Missile III's 11 (5.5 versus armor) at 600 range, and are reduced to 6 damage per shot at 700 range. For the size invested, the missiles also tend to remain better DPS-wise at standoff ranges. If you're looking for a standoff weapon for early-game to mid-game designs, missiles are neither terrible by comparison to torpedoes nor all that expensive to develop or deploy. Even if you switch over to Velocity Shards (or even Shockwave Torpedoes, though I'd consider those more of a mid-range weapon than a standoff weapon) in the mid-game, devoting a bit of research to missiles early isn't going to put you that far behind. Torpedoes are simply 'safer' weapons because from the mid-game onwards they can maintain their short-range DPS and damage per shot advantages over missiles at progressively less short ranges.
What kind of cruise/sprint/turn speed should I shoot for with 300ton ship? (As I understand it combat is conducted at sprint speed but forum posts seem to talk in terms of cruise speed which is puzzling to me) I've seen post where people target 45+ but that leaves little room for fuel/1 weapon.
Regardless of the ship's purpose, I aim for a minimum cruise speed of ~20 or so; you require a cruise speed of around 12-15 in order to catch up to a planet when out of fuel (planets move at something like 3 or 4 speed and being out of fuel reduces your ships to one third of their design speed; sprinting only occurs in combat, and impulse speed, which is unaffected by fuel or installed power as far as I know, is only used for actual docking maneuvers and fine-tuning the position the ship stops in, so a cruise speed which is at least three times greater than a planet's movement speed is necessary unless you want to fiddle with jumping around or specifically order the ship to a station in a gas cloud rather than relying on the 'refuel at nearest X' command to be smart about where it sends the ship). ~25 is probably pretty decent for an early-game size-300 warship with ion thrusters; 30 would be better, but it'll cost you more (specifically, 3 or 4 additional thrusters to go from a cruise speed of ~25 to a cruise speed of ~30 for a size-300 ship propelled by Ion Thrusters or Proton Thruster Is). Once I get better thrusters than Ion or early Proton Thrusters, I tend to shoot for a minimum cruise speed of ~25-30 for most designs, though very heavy warship designs may have lower design speeds. I don't really have design targets for sprint speeds; they're tied to cruise speeds through the thrusters I have, so a goal for one effectively sets the goal for the other.
As far as turning speeds go, I tend to like ~5 vectoring thruster components, though I'd keep an eye on the actual turn rate; the turn rate formula appears to be something like
6 + 115 * [number of vectoring thrusters] * [thrust per vectoring thruster] / [total ship size]
so if your turn rates are pushing down close to 6 degrees per second it may not be worth having the additional vectoring thrusters on the design (alternatively, it's past time to upgrade to better vectoring thrusters and maybe add more vectoring thrusters). You need to keep at least 1 vectoring thruster on the design, of course.
As far as getting ships up to 45+ cruise speed, the difficulty of doing that depends on the thrusters you have and how much you're willing to invest in thrusters. TurboThruster Is can manage it on a size-300 ship with 16 drive components (112 size, cruise speed of 45.3), and Starburner Is can manage it on size-300 ships with 12 drive components (84 size, cruise speed of 47.2), though these are among the best drives in the game in terms of attainable speeds; generally available components won't begin surpassing these tier 2 racial techs until you reach Vortex IIs or Acceleros IIIs (the earliest common drive components to surpass the TurboThruster I in cruise thrust per size and thus attainable speed, though they're still not equal to Starburners) or Vortex IIIs (the only common drive component to surpass the Starburner I in cruise thrust per size and thus attainable speed); if you want to trade components at 1-1 rather than size at 1-1, then the Acceleros II is the first common component to surpass the TurboThruster I in cruise thrust per component, though the Vortex Engine III is once again the only common component to surpass the Starburner I.
Personally, even my heavy ships normally don't see more than ~30% of their size invested into defenses and another ~30% of their size invested into weapons (rough estimate, based on a quick survey of the designs I've created in the save games I've kept), so there is some space available, especially on lighter ships, if you want to pursue these kinds of speeds, but it's very helpful to have access to the better thrusters if you want to manage this, especially if those thrusters have been upgraded to some degree.
I really want to love Titan Beams but the Torpedoe design was my most effective and you've seen it. Any tips for building close range military ships (or should I just focus on Standoff ships)? They obviously need to be tougher (shields/armor) and faster but finding the balance between the two is not easy.
Try something like 20% of the ship's size invested in blasters, 30% in defenses (so ~90-100 size units on a size-300 ship; perhaps 8 shield generators and 15 armor would be decent), the rest into thrusters, reactors, hyperdrives, and other required components, see how it performs, and experiment from there to see what you like. If you have phasers (either cannons or lances, though I prefer lances for the range), you might consider mixing a few of them in with the blasters to improve anti-armor performance. An early design with bad reactors may need to cut back on the armament and defenses in order to achieve an acceptable speed (30 would be good early on, but 15-25 is probably acceptable if your intention is for the ship to be able to drive off rather than run down and kill opponents).