I'm late to this discussion since I only joined recently but have thought about this topic a bit. I prefer the TV schemes in a lot of ways, but I agree that the movie schemes are more realistic from the standpoint of military uniformity. I think the TV schemes are more "classic mecha," being fully-repainted in the case of Max and Milia's aircraft, but the small patches of color on the movie Valkyries are more practical, while maintaining their squadron theme. I also agree with the earlier post about the Max and Hayao Kakizaki VF-1As' personalized paint schemes in the series being a little unrealistic, given that they were brand new pilots, but I understand the practical need to identify the characters during the battle scenes.
On a side note, I'm fascinated by all the squadron-specific paint schemes in the Master File books, having just bought my first two. I hope to recreate several of them using Hasegawa 1/72 fighters. I'm in the military in real life, so I've always liked the basic soldiers in the series, the "cannon fodder" brown VF-1As (hence my name and avatar). I plan to build several of those, but I'm curious about them in light of the squadron concepts presented in the Master Files. I guess the idea is that the VF-1As are mass-produced in the brown and white paint scheme and then repainted into specific schemes by the operational squadrons. However, the Master Files would seem to imply that there wouldn't be any brown VF-1As left on the SDF or the Prometheus (except for the squadrons that are variations on the brown scheme), which obviously isn't the case. I'm probably overthinking this...
Can anyone tell me the back story behind the Sonic Birds, anniversary, and the low visibility schemes that Hasegawa offered on their fighter model? Were those first created by Hasegawa and then included in the Master Files, or the other way around? I know the Angel Birds appeared in the TV series, but I don't recall any of the others. I would love to see decals produced for the other squadrons in the books. I know Hasegawa offered some extra decal sets, but from the photos I found online, it doesn't look like they correspond to other squadrons included in the Master Files.