Speaking of missile reload times, I'd suggest giving the single shot missiles a relatively long reload time - make it so that the +1 ammo skill perk is more "you get a second shot" and less "you get to spam out two of these for double damage when you decide to fire".
I am uncertain on the beam changes; will have to see how those play out. That said, I am slightly worried about beams having longer ranges and not being stopped by missiles when used as PD - I foresee a high potential for friendly fire incidents.
I would strongly suggest adding a "soft flux" flag to weapons and corresponding Codex information - it would really open up some interesting options (especially for modders) if we could have, say, ion cannons & salamanders dealing soft flux, or have one or two beam types that deal hard flux (maybe that could be the niche for the HIL now that it has lost its range?)
I agree that the loss of ammunition from ballistic weapons is a big thematic hit - and also agree that they need to have ammunition that's not a long-term limit. Short term, however... I'd like to see ballistic weapons that have limited ammunition and ammunition regeneration, with the expanded magazines hull mod increasing both capacity and regen - some of the smaller ballistic weapons (and especially point defense weapons) with the hull mod should just never run out of ammunition, while weapons that are currently very ammo-limited (gauss cannon, for example) would still be able to run short for a bit in heavy combat.
I'd also like to see reloading for ballistics happening in chunks - this isn't the "clip reload" mechanic you (rightly) disapprove of, just a cosmetic thing: instead of regenerating one shot every second (for example), have it regenerate 10 shots all at once every 10 seconds - especially important for theme if you have, say, a light machine gun that (with the expanded magazines mod) literally can't run out of ammo; you'd see ammo decreasing until it hit its reload time and then jump back to full.
CR changes... not so keen on this; I've eschewed frigates since the CR timers went in in the first place, since my preferred play style is to pilot a single ship. Can we get at least a few specific vessels that - like the Brawler - don't have CR timers? Will wait to see how it plays out, but right now not a fan; yeah, I can swap to flying a Conquest or Onslaught or Paragon, but I'd like to have a few more options than just those three.