Air R&D
After nearly four months of war, I've settled on my final R&D program for this game. I'll give an overview of it and my reasoning behind it, as it's changed some from my initial projections.
IJN
Fighters
A6M3a Zero - 1x30 - This is moving on to the A6M5c
A6M5 Zero - 3x30 - Two are converted Rufe R&D factories, they'll be moving on to the A6M5c line shortly. Once the 5c is nearly operational status I'll move two over to the Sam.
A7M2 Sam - 2x30 - Will be bolstered by two more factories once the Zero 5c is online. Late-war IJN CAP and CV plane.
J2M2 Jack - 1x30 - Will repair and move the M2 into production, then bring the M3 forward, then on to the M5.
J2M5 Jack - 1x30 - Should be the M2 model, misclick that has cost me supplies! Will go into production.
J7W1 Shinden - 3x30 - Late war IJN CAP.
N1K1-J George - 4x30 - Will repair, two factories will produce the K1 model, with two more moving the progress if the K2 and then K5 models forward.
Everything Else
B6N2 Jill - 3x30 - Will go right into production. I don't see the value in bringing the N2a model closer just for radar that only actives on 10/44. Will replace the Kate until the Grace arrives, then it will be an exclusive land-based airframe.
B7A2 Grace - 3x30 - I like this plane. Will go right into production and I plan to use it as the exclusive strike aircraft on my CV's.
C6N1 Myrt - 1x30 - Will go right into production as the N2 model is inferior. Amazing range for search and deep recon.
D4Y1 Judy - 4x30 - All will move to the Y4 model once repaired to get this airframe into action ASAP. Will replace the Val on CV's until the Grace arrives, then land-based use after that.
D4Y1-C Judy - 1x30 - Will go into production to tide over the IJN recon squadrons till the Myrt arrives.
H8K1 Emily - 1x30 - Will go into production. The K2 model arrives in 3/43 and gets a radar that doesn't active till 6/44.
H8K2-L Emily - 1x30 - Crazy range, crazy load. Will be the main IJN transport.
J1N1-S Irving - 2x30 - Not an amazing NF, but it arrives early. One factory will go into production and the other will switch to boost the P1Y2-S NF.
P1Y1 Frances - 3x30 - Replacement for the Betty/Nell. One factory will convert to production (and all remaining Betty/Nell production switch to Frances) while the remaining three factories push the Y2 model forward.
P1Y2 Frances - 1x30 - A third misclick

I like this for the service rating of 2, even if the speed is lower.
P1Y2-S Frances - 2x30 - Mainstay IJN night fighter, will replace the Irving. Big, durable, has radar and armour and is slower than a B-29, I want this night fighter to just sit around all through the night to irritate B-29 raids.
Toka - 4x30 - Much like the Ki-115, this isn't a very good plane, but it's vastly superior to the biplane and monoplane trainers that arrive en-masse in the late game.
IJA
Fighters
Ki-102a Randy - 3x30 - Late war IJA fighter. Good all round plane so I want it in '44.
Ki-43-IIa Oscar - 2x30 - Will bring the IIa online then move up the Oscar tree, bringing each model online till it reaches the IV.
Ki-43 IIb Oscar - 1x30 - Another misclick, this time not as expensive. Will move to bring this line online up to the IV.
Ki-45 A Nick - 1x30 - Online in less than a month, and will go right into production. Will bulk out the IJA's frontline strength for the duration of the war. I don't like the Randy FB as I feel it's a marginal improvement.
Ki-61 Tony - 3x30 - Once repaired, will rush for the Ki-100-I Tony to get that online ASAP.
Ki-83 - 4x30 - Lots of potential for this big late war sweep/escort machine.
Ki-45 D Nick - 1x30 - Mainstay IJA NF model. It was a toss-up between this and the Dinah, but the Dinah is less durable and without armour, so the survivability of the Nick wins out. Will go right into production as the sole IJA night fighter. The Randy C just gets in too late.
Ki-84a Frank - 4x30 - Can't do without the Frank for the IJA. One factory will convert and the other three will push for the R model.
Ki-94 II - 5x30 - It's a beast of a late-war fighter. I like this ASAP.
Everything Else
Ki-48-IIb Lily - 1x30 - IJA dive bomber, will go right into production and all existing Lily production will convert to this model.
Ki-67 Peggy (T) - 4x30 - Big push for the Peggy T to give the IJA torpedo capability and to phase out all the older level bomber models.
Ki-74 Patsy - 4x30 - Nemo talked me into this. I'm not fully convinced, but I'm willing to give it a shot. It can hit out to 36 (!!!) hexes, so I hope to use it as deep raider or in the kamikaze role from rear-area bases. The massive range, good speed and absurd max altitude on this plane has me very excited about the possible tactical uses of this aircraft in the late gaem...
Ki-115a Tsurugi - 3x30 - Will move all to the 115b model. Late war dedicated kami. Not a great plane to be honest, but it's a massive quantative improvement for those squadrons that arrive using the Stella.