The one gripe I have with double-clicking is that it doesn't select the various upgrades together, but I don't think it can be fixed.
I personally understand each upgrade as an independant ship to the engine, despite the "is variant of" tag I've seen. Not that I've done much in the way of modding this game. Ctr-A is what bugs me; it groups MC-120s and X-Wings together at random.
I managed to pull off a popcap of 127 space wise without too much dangerous lag, but after that, managing is limited to Ctr-A and just pointing where the enemy is; its too complicated otherwise with all of the fighter spawns. Smaller ships (DP-27...) can't be selected at all. Seen as many as 5 Praetors at once too...
Also, how come your AI uses Sovereigns? Mine won't upgrade anything, even with the new Zarkis mod and a new game. How long did it take them to get it?