I haven't had any issues with air units not having enough fuel to get across the maps and go into battle. Some do better than others, but I've never had any with functional problems. Dunno if that might be due to a later update. Even still, I do like the fuel aspect cause it requires you to make choices, even if the usage of fuel is not on a realistic scale.
I will not argue that the artillery and nukes aren't underpowered. Then again, the same is true of TA if you think about it. Both games take place way way way in the future. Despite this, both games have a very 20th century approach. In neither case would this be reasonable, just as the whole Warhammer 40K universe seems awfully messed up.
Point being two things: 1) The creators are very much limited by their knowledge and imaginations. They wanted to go the strategic routes they knew, which is a trap when dealing with future tech. 2) They wanted to make a fun game. Without pushing the boundaries of memory usage, they could not make a map large enough to truly see everything from ground units to ICBMs come into play. Some things had to be pumped up and some things brought down. More than anything, it does have to be fun and balanced.
With the exception of the air unit issue, that's why I play with artillery and nukes off. This way I'm forced to pick my battles and move against the tide for every inch I gain, with neither myself nor my opponnet taking the easy way out.
As for SupCom2's experimentals: I just feel that after a point I don't end up building any normal units, just armies of experimentals, which sucks given that the research concept practically goes out of the window at that point.