As they say, you only learn when you lose. So I'll skip the praise (good job, btw), and go to the suggestions:
Soviets:
1. The Reaper has become completely redundant. It can't even hit a moving Kirov without the homing, not to mention a Vindicator or Twinblade. And it can't force fire at the sky. What I propose is, either scrap the reaping issue from the game and use the model as a component/enhancement for an existing unit (apoc?), or get rid of the proto jump, and turn the Reaper into a MDV (Mobile Defence Vehicle) that has as high a defense as a VX defender, and the ability to deploy and undeploy repeatedly, like an MCV. Undo the grenade and missile changes (they're totally ruining the Reaper) and make the grenade more effective against infantry ( 1 volley KO). Either replace the Missile rack with a precision rocket turret


2. Nice V4 rocket speed boost. But I was wondering if you could give the V4 precision rocket a slightly larger AOE, or make it look as though it had a larger AOE. And could you please improve upon the explosions of the cluster bombs. They feel rather weak, even though they are good.
3. The desolator is still pretty useless as an anti-armour unit. Would it be possible to fix it by giving the desolator splatter thing an armour cancellation ability or a property that specifically increases the death spray's damage incrementally over time (like damage acceleration, not unlike the King Oni)
4. It is impossible to safely expand the normal way (packing up MCV and moving to expansion) without encountering the radar off-ing problem. It is very severe as sputnik expansion is not feasible early game. I suggest creating a radar structure that will serve as an alternative to the MCV as a Radar enabling structure (meaning, {either or} the Radar dish or the MCV has to be up to maintain the radar)
5. I am very impressed by the MiG's improvements. The attacking speed is just right. What needs working is now it's maneuvering. Is it possible to allow the MiG to move in a straight line as per vanilla when it is pursuing fast moving objects, and make those loops ONLY when it is significantly faster than the target such that it is always overtaking it.
6. Minor snag: Tsar Bomba always makes my com lag. Can you reduce the smoke?
7. Twinblade rockets have Neutron star effect. Making them drop, then home in on the location in a trajectory like a negative quadratic equation would be more realistic. This might need a larger range for the Twinblade's rockets as a by product. Then again, hellfire rockets have very long ranges on Apaches.
8. Make Kirov bigger?
Japanese:
1. I don't see the necessity of the Greater King Oni. Seems to be just some fancy addition like the Reaper.
2. I think I suggested once to allow the King Oni to climb cliffs? Is it possible?
3. Very good changes to VX striker. No longer so OP. You might want to increase reload time, though. Just a little.
4. Shogun battleship shell FX disproportionate to the damage it does, as is the Giga fortress.
5. Wave force artillery maximum charge up FX disproportionate to the firing FX. More bloom, fatter beam and a nice Neutron Star explosion at the end of the beam would be very filling.
6. Giga fortress landing splash FX error. Splashes before it hits the water.
You might want to try letting the Giga fortress transform in the water, then lifting up. Just for reality/fun sake?
7. I like how you've slowed down the transformations for VX Striker and Mecha Tengu. For balance, you might just want to slow it down further. 1.5 to 2 secs maybe?
8. Love the dewy Rocket Angel attacking FX. Mountain dewy!!
9. Giga Fortress reload time too long, and damage slightly low. Makes Giga fortress disproportionate, less useful and considerably less desirable. It's hard to explain, but giving the Giga fortress strategic weaknesses rather than nerfing its fire power is more appealing gameplay wise. See below.
10. Suggestion: tie the Giga fortress to the power supply. If you can, perhaps make it such that infiltrating or destroying the Nanocore Mainframe will disable all Giga fortresses? Would balance out the above suggested firepower increases.
Allies:
1. Pacifier FAV is just TOO inaccurate. It doesn't even change it's direction after the target has moved far far away! The damage is also too low. It took me four Pacifiers to destroy a refinery in the same time as vanilla.
2. I don't get the chronotank's proton attack. Isn't it too powerful and inconsistent with Chronology?
3. Harbinger is too accurate, and reload is too fast.
4. Was the damage of the Future tank decreased? Seems like it.
5. Could you please make the Proton Collider's damage increase not with the number of walls, but buildings? I suggest making powerplants explode would be good as a damage increasing factor.