I like your suggestion about point 1 CornhuskerMac, upgrading in deep space is a bit silly and would probably be very expensive. Actually I wouldn't mind not being able to upgrade at all if a ship isn't in orbit IF upgrading IN orbit would be reasonably priced.
I usually use one light fighter on each planet to guard for invasions/pirates/vengenance fighters etc. and I would like to be able to keep them up-to-date by upgrading all my fighters.
Point 3: I know that in the calculations ships fire simultaniously. I think this was implemented to counter the cheesy tactic of using interceptor cargoships loaded with engines and weapons. But I still think it would be nicer to be able to have the shoot first option for two reasons:
1. tactical decisions: evasive maneouvres or try to attack first?
2. fun: being able with a superior fleet to wipe out an enemy fleet, never giving them the chance to respond.
Point two could be made less harsh maybe by incorporating rules for different hull sizes for instance. So that large battleships have trouble targeting nimble fighters, so that it is very difficult to kill an enemy fleet in one strike, making the interceptor cargoships an unattractive option. You would be able then to kill a fleet in one strike only if you have small fighters, or if you have light but fast targeting weapons on your battleship. This would make one-strikes possible but hard to get and in general making ship battles a little more interesting perhaps.
Of course, the fun of this depends also on what one could consider realistic space-combat. This is just my version, it's probable that future space-wars are nothing like WWII naval battles/Starwars at all and so utterly boring (and soundless) that future Galactic Civilizations play Galciv for the highest score to settle Galactic disputes.