1. Upkeep model- I'd say lowering upkeep & movement costs but increasing production costs would improve things a lot. Right now initial production costs are extremely low but upkeep/movement costs are extremely high (25% production cost in upkeep per turn). You're never too broke to make new units, you just can't afford to upkeep or move them. So the computer keeps pumping out annoying ships every turn I have to kill even though it can't afford to do anything with them.
The high upkeep also makes for some bizarre economic decisions. Normally if your unit got damaged in a game, you'd try to pull it back for repairs, right? Here it's totally not worth it. You pay 1/4th a unit's cost in upkeep per turn, so why would I ever spend 6+ turns moving it back to base and waiting for it to get repaired? Plus there's the cost of moving it to and from the front. It's just not worth it. You're better off just self-destructing all your damaged ships and building new ones (unless the experience bonus for ships is really really huge). You also never want to outright destroy enemy ships. Just damage them enough so they have no attack strength then move on. Going in for the kill is a bad thing
There's also absolutely no reason to maintain a standing ground force. There are only two circumstances you'd ever want to builld ground units: the very moment right before you're about to invade and right before you're about to be invaded. You can build a large ground force in a single turn, you always get advanced notice that the enemy is coming, so you can ignore having any army until a troop transport you can't stop is right on top of you. Ground troops cost a ton to maintain (mechs are more expensive than cruisers??), so scrapping them all right after a ground battle is always the best bet.
2. Gold & fuel are the only useful resources: Ore is only required for initial construction, and since it's never higher than the fuel cost, ore will never ever be the limiting reagent. Food is pretty much only used by ground forces, and since it's best to scrap all ground forces immediately after they've fulfilled their use in a ground battle, food is never an issue. Fuel gets burned up in movement faster than crystal so crystals are never really an issue. Planets that produce more fuel (volcanic?) are much more valuable than planets that specialize in other resources (the food producing planets are by far the least useful).
I'd say, along with increasing production & decreasing upkeep, make each resource the primary factor for something. Ore can be the unit production resource. Gold can be the upkeep resource. Food the ground forces production/upkeep resource. Fuel the ship movement resource. Crystals can be the.......research resource? I dunno. Or change it around so each race's units requires different resources (Fvost: crystal, etc.)
3. Minor unit balance issues: The Fvost mechs that freeze units are the best, while the missionary and plague mech are useless. The missionary mech is insanely expensive, and has to get close to convert, so to be worth it he'd have to convert any unit. Right now he can only convert infantry and snipers. For the missionary's space and cost, I'd rather just have 6-9 addditional infantry. Re: the plague mech, he'd be worth it if every unit under his area of effect was guarenteed to get poisoned, but it seems there's only about a 25% chance of that, so you only end up poisoning about one unit per turn, which isn't worth it at all.