The Marshalls has a lot of small islands, most of which are semi-worthless as airbases. The biggest (IIRC) size of airbase that you can get in the Marshalls is size 5, and even then only on a handful of islands and with significant effort.
Given the small size of airbases in the Marshalls generally, owning and being able to use a size 5 airbase to contest against an opponent using smaller airbases gives a considerable advantage.
In SWPAC, airbases can be built up much further, and with much less resources. Here, even the dot bases can normally be built up to respectable sizes, and an opponent can contest the airspace with a greater degree of ease.
There's also much more bases point blank, which changes the dynamic from quite a linear campaign from the Gilberts to the Marshalls.
You remember correctly. Alinglaplap has max AF of 5. Then there is also Tabiteuea which is a potential 6.
Regarding the questions of the thread.
I think that the air defences in 42, 43, 44 and 45 are terribily different and each part of the game is a whole different beast on its own.
Avoid trash atolls that bring you nothing and that are impossible to defend. Great example is Canton Island, which is a little atoll in the middle of nowhere and the allied player can approach it simply developing dot after dot.
If you defend an area such as Tabiteuea, it's easier: more decent AF around, good supply routes, wonderful SL.
Interpret the game in your strategy. Are you focused on a decisive battle somewhere in 43? In 44? Are you going to do a staged defence to bleed out as much as you can the allies or you'll adopt an all-or-nothing approach? Etcetc.
For example: I am very inclined to focus my industrial production, R&D and forces disposition in order to fight a decisive battle somewhere in late 43 or early 44. It's highly unlikely that my allied opponents will show up with relevant forces I can engage before that date.
Therefore, I am a stingy bastard in terms of pilots, airframes and ships. I prefer to lose an air battle in 42 using crappy pilots but having the good ones in the reserve, rather than having 100-0 in the skies in 42 and then fight with rookies later on.
On the other side, if you have a different strategic approach, you are for sure right in keeping a stronger airforce in 42.
Therefore, it all depends on your basic strategy and your doctrine.
Since you are a lot into island defence, here is my advice: check the bases that are further away from the allied positions. Tabiteuea is a good example, since the allied player cannot really start developing one dot after the other approaching it. It's relatively far from potential bases.
Then, try always to think in terms of mutual support. Tabiteuea, the example, has great SL (40.000 IIRC), good AF, good port. Now, the main asset of the base is that it has various good bases around you can develop.
A group of bases is useful because:
I) the enemy has to put considerable efforts to close all the AF
II) there are safe places where planes can rest / substitute losses
III) it might be the case that the allies cannot recon them and see what's there
IV) you are always able to pose a potential threat to any action undertaken by the enemy with token forces.
Regarding Point IV: in Tabiteuea example, the allied player can put relatively few bombers in a base, trash your AF and land somewhere with few troops. If you have a strong set of various bases, he can do the same (it's not that hard to close various bases for a couple of turns), but he has to bring a lot of stuff to do the trick. That's the point. He cannot just blitz, taking advantage of a temporary superiority.
As mentioned, Rufes are your friends. Definitely useful to shot down pesky Catalinas and to disturb bombing runs.
I don't use any fighter on Pacific Islands since I find positions over there too exposed and I firmly believe that if you put enough distance between you and enemy's (potential) bases, you are just fine. If US Carriers intervene, you are screwed whatever you do, so what's the point?
However, rufes are very very good substitutes of fighter presence.
Positions can be defended in a very strong fashion if you don't overextend. Take Marshall Islands. You have various bases with 6.000SL plus Mili and Alinglaplap which have 10.000SL. You can pretty easily pack 1 SNLF + 1 NavGuards + 1 AF Coy + whatever 4th unit you want in the small islands and have a more relevant presence in Alinglaplap and Mili so that you basically oblige the allied player to assault multiple bases (what does he do with just, say, Jaluit?!). Forts lvl 4 or even 6 aren't that expensive in terms of supplies and they do save your @ss in these small places.
Not a single SR3 fighter should even approach the Pacific. That's my rule. I am open to use them in Rabaul area until it's operational and eventually in the big show in Mariannas.
Regarding AAs. For most of the game, until the Allied player is approaching Onshu, I use them in huge concentrations in key locations.
In a PBEM, for example I have 25xAA at Rabaul and 25xAA at Magwe. This is roughly 50% of the total amount of AAs you have. Just for two bases. My logic is quite simple: few losses won't prevent the allied player to pursue his objectives, while a strong attrition can instead make him change target. And, especially, in case my CAP f@cks up getting slaughtered, I can somehow still defend the base for a while without having a breakdown in the front.
In some places I put sparse AAs just because I want to create a little bit of attrition to the enemy in case he goes with low bombing on my units. The typical example is represented by my line of RTA Divisions in the jungle at the Indo-Burmese border: each unit defends an hex and they have a battery of 75mm just to shot down few allied players when they bomb them.
Other examples are some atolls in which I place SNLF and AF Coy which have a 40mm in the TOE. It upgrades to the 20mm, which can be seen as a better weapon, but I do prefer the 40mm and therefore I set on "no upgrades" and I purchase whatever unit has them (mainly various SNLF in China). The idea is to have few shots to enemy's dive bombers if he does some raid to trash atoll's installations. For this purpose, I also use the 4 (or 5?) MGCo or something like that that are present in Manchuria: they are units with 6x20mm in their TOE with negligible SL and they are quite good if you want to put a token defence on atolls. DiveBombers always get few losses and I deem it a good ROI (few PPs and SL for few US CVs' DBs... Fair).
Last but not least, don't forget these three things when setting up air defences around:
A) possibility of redeployment
B) LRCAP / leaking CAP
C) whatever is on the coast, it's lost
A) is a complex topic and it encompasses both the possibility of moving the a/c in case the AF gets trashed and also the strategic situation. If you have 200F in the Marshalls and the enemy attacks Timor, you'll want for sure the Oscars-IV and their amazing range, not the Tojos.
B) LRCAP and leaking CAP are good techniques to fight bombing runs without exposing yourself too much. A typical example is an allied player who destroyes the AF in Rangoon and you defend the city via leaking CAP from Pegu and Bassein, so that you avoid the nasty situation in which you lose the AF and then you get the port and the infrastructures destroyed.
C) naval bombing is always undervalued but it's the main element in my decision making regarding which AF is gonna be used and which not. For example the base at the center of Hokkaido is amazing since it's plain but it can have an AF lvl 9 and it's the only base not on the sea in the island. It means that the enemy cannot shut down the AF via naval bombing.
Same in Thousand Ships Bay, remarkably forgotten dot north of Tulagi. The funny dot, instead, can be easily protected putting AMC in all the surrounding bases plus mines. Allies will have a complex route to bomb the base through the only non-mined, open-sea hex. In general, I take for granted that whatever is on the coast, will explode in a column of smoke due to naval bombardaments. Another interesting position in the Pacific Theater is represented by Saidor and Long Island if you protect the Vitiaz Strait. I always do and it's quite effective, at least in avoiding sudden naval bombardaments which leave your planes damaged in a base without railway and exposed.