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I have always wondered why Japanese base forces are so puny compared to the allied side, especially when it comes to air support.

The two big ones that begin the game - the 4th at Truk and the 8th based at Rabaul - are certainly big enough to maintain those bases and sustain a respectable air campaign, but past that the capabilities really drop off. The remainder come in with only 40 air support points each, barely enough to maintain a fighter and perhaps a Val or Betty/Nell squadron in combat. I find it necessary to pair up base forces just to get an adequate level of support for places like Lae or the Shortlands, and there really aren't that many to go around.

The allies, on the other hand, also come in with a couple of big base forces (three if you count SOPAC's organic air support), but these are complemented by a significant number of decent size units of 120 / 150 points each. That is enough to convert a field like Gili Gili or Irau to an offensive base to be reckoned with.

Even the smallest ones with 60 points can still take care of two fighter and a recon / or bomber squadron by themselves.

So why the disparity?

historically, the Japanese lacked virtually everything in their Southern areas. Fuel, spareparts, medicines (no DDT!), just most of any stuff was scarce. So with adequate ENG personnel. Though some of the reinforcements that were sent down got lost while underway (to US subs), they were far undersupplied from the begin -compared to their allied counterpart...

Maybe in the game this is programmed a little bit too unfavourable for the Japanese, but in general I guess its more or less realistic.

Of course you´re right, this is hampering your offensive abilities & assets as IJN player. Usually, you can run only two...three big airbases (>250 support) plus some minor airfields.
This isn´t a problem anymore after spring 1943, since the allies will strongly cut down the number of your A/C then... Its always a good idea rather to scatter your aircrafts & base units instead of concentrate them at a few points. Remember, the US can close an airfield with their 4Es very quickly - and for long! It´s pretty regrettable to see 300+ planes getting stuck at Lunga with almost no chance to escape... [:-]
Only if you´re really good in fighting down the allies and keeping them at bay for long, you will get into some troubles (where to base all these planes coming down from Japan?). As for me, in only one (PBEM) game I was glad enough to experience just that. Otherwise, please "waste" your A/C before the Allied steamroller will kill them on the ground... [;)]

just to make it complete:

the IJN/IJA receives 680 air support during the game (840 in Sc19), plus 440 already in the theatre at May 1st. Makes 1120 (1280 - Sc19) alltogether.
As one can see there is no opulence with these units... It´s a painstaking issue to maintain any kind of a "rotation" of worn out base forces back to Truk (the only base where they will recover).
And loosing one or even more of them is really not funny