I was playing some strategy games on the comp the other day and was musing about this game when something came up in the dusty old attic of mine: why not bundle units together and make their upgrades tied to each other?
An example would be upgrading Air Systems- one upgrade would use some turns, some cash, but would upgrade bombers and jets. Missile systems would upgrade both SAMs and attack missiles. You could always leave ships/spies as is, taking less money/turns to balance it out (only one unit being uprgraded here). Ground systems would upgrade inf and tanks.
You could always go all out and do a single costly upgrade that makes everything go up a level. Prices and turns would need tweaking no doubt, but it could work.
Eliminate the per unit cost while upgrading (flat price) and people will be able to maintain defense while going about their business. I know the newer players would enjoy it since its one less thing to worry about. With the new unit and new attacks, it would simplify everything for everyone without having to retool too much.