I support the elimination of ammo, it's "cool" from a mechanical standpoint, but from a game play standpoint not so much other than "oh crap I just ran out of ammo didn't I, ugh, better retreat!"
Also very cool to see regenerating missiles, it makes sense, given that the crew is probably running them in from storage (or machines are fabricating them on the fly!). Would be neat for it to stop below a certain CR. Also my carriers will no longer float around uselessly once they've expanded their 30 Pilum.
The overall weapon changes, not sure! Will have to see. I'm really going to miss the Flux charge, I fly an energy fleet (when possible, lol grr) and seeing the weapons heat up and fire is just really cool. I don't know about a balance standpoint, it just seems really cool honestly and a well thought out mechanism, and I'm sorry to see it go just for novelty sake. Unlike other posters I definitely DO notice a difference, especially when it starts maxing out, tactical lasers mounted on your Wolf can literally melt low tech frigates with +50% power boost. Maybe Beam weapons keep their flux boost. It would actually make sense given their new longer ranges, the beams crystals become superheated or something. Given that they don't do tremendous damage, they might allow to keep flux charge without too much imbalancing.
I would also agree that although it's good for game play it's sort of sad to have ballistics lose some of their distinctiveness with no ammo limit. Maybe certain guns have a tendency to malfunction when they fire for ridiculously long times, I'm thinking the needlers and vulcans, though I guess needlers have a built in burst size that limits their overheating (not sure)
Maybe to make ballistic more interesting a third fire mode can be introduced just for them (alternating, linked,
overheat) which is basically the guns fire at higher velocity but at lower accuracy and a chance to temporarily malfunction (jam). The jam chance is reduced by CR, but is always possible. I know you can say (ballistic does damage to shields, high ex to armor, they're distinct) but there's distinct tactically and distinct personality, which is why I also think you should keep flux boost to at least some energy, it's cool