1. This would be awesome but sadly is impossible - a craft cannot be upgraded since it's named & numbered. So each upgrade would have to be built from scratch. But a Skyranger research tree... yeah why not, I'll think about it, after all, it has one advantage - no Elerium dependency. And if you sell the Bonaventura to buy Skyranger, you're $2M richer. There is a problem though - it's a jet and the jet technology has gone backwards between 1990s and 2600s - elerium-powered crafts are plentiful and vastly superior so why worry.
This makes me think... of course I know that Bonaventura is so good there is a wasted "getting better ships" potential here... but then again, it has to be that good because the game is hard. Either that, or we could switch it to a super-crappy transport (even below Skyranger level) + a very tough (but slow - 2000 speed or so) fighter in 2nd hangar... I don't know, I got used to the current arrangement, but maybe the drive to get a better transport could provide more fun?
2. I thought about it, but... it'd invalidate the knives, and it'd also create a "best of both worlds" soldier equipping pattern... sword + 2-handed gun... why bother with pistols? Even worse, a 3x1 slot could hold most long arms...
3. Definitely. It'll be either that or advanced (manufacturable) mortar, but 200 HE elerium shell will be added.