Unlimited Ballistic Ammo & Regenerating Missile Ammo
Personally, I don't like these changes one bit. And here is why. But before that, you need to understand how I play, and you'll most likely see why I don't like the changes at all. I play as a bounty hunter, at most 2D+1F fleet, rather small so to speak. I am able to take on pretty much anything in one go, except fleets with capital ships, which requires me to fight a battle of attrition.
Attrition you ask? If the enemy capital ship has a lot of ballistic/missile weapons, and just a few energy weapons, the battles sometimes drag on a lot. First thing I do is get rid of any escorts, then let the capital ship run out of ammo. When the enemy capital ship is out of ammo, most of the time it is forced to retreat, where I keep pushing on and eventually they have just a little bit of CR left, while I still have loads. Malfunctions here and there on the enemy ships, while mine are working fine. And eventually the enemy succumbs to the pressure.
And enemy missile boats. Have you seen a lot of these, and them firing at the same time? Lower your shields for a second, and you are dead. Overload, and you are dead. Keep your distance, be patient, and enemy runs out of missiles, which is an opening you've been waiting for. Also, I've run out of ammo more than a few times, which forced me to retreat or call in reinforcements. Contrary to what people thing, you can run out of ammo.
I can talk about many other examples that changes gameplay just because some weapons have limited ammo. But these examples have one common point: small fleets trying to take on bigger ones. Small ships trying to take on bigger ones. So my suggestions are: don't remove the ammo limit; don't make missiles regenerate. Instead, if you really want to adapt these, add two hull modifications instead; one for each, which would manufacture ammunition in combat. But make ammo limit still count for something, even if these modifications are present on the ship.
Flux-to-energy damage
I also don't like this change. Whenever I am using energy weapons, I often try to stay on high flux zone in order to receive a substantial damage bonus. One wild volley hitting my shields would mean overload for me, but that is the price to pay. More than 50% of the times that I am exchanging fire, I am well over 50-60% flux in order to get a bonus to keep the pressure on the enemy.
The main reason
The main reason I don't like these changes is, it takes away what makes each type of weapon unique (flux bonus for energy weapons, limited ammo for ballistics & missiles). I really think it is a mistake. We can always get a mod that "reverts" these changes, but still, please consider what you are doing.