With Wave 1 out, we have the start of our new ship meta. But let's talk upgrades! Several upgrades are very much a 'one or the other' sort of deal. Some seem more obvious than others but generally have similar roles.
Off the top of my head, the most obvious ones are:
Ordinance: Assault Concussion Missiles vs Expanded Launchers
Defense: ECM vs Advanced Projectors
Turbolaser: X17s vs XX9s vs Enhanced Armament
Ion Cannon: Leading Shots vs Ion Cannon vs Overload Pulse
Support Team: Nav Team vs Engine Techs
I think that most of these are alas fairly clear cut.
Ordinance: ACMs are more powerful than expanded launchers in general, especially if you get two arcs. They really are damned good and cheaper.
Defense: ECM is really vital for the ships that carry it. Adv Projectors are good, but currently ECM is more needed
Turbolaser: Enhanced Armament is great, but X17s are cheaper and affect all arcs. Even call. XX9s seem too much 'win more' to me.
Ion Cannon: Leading Shots increases your offense output very easily and is cheap. The others seem too gimmicky.
Support Team: Engine Techs costs more, but is better than Nav Team for the most part.