Even in X, the Mass Drivers were a niche weapon. Especially in X2, in X3 they were somewhat better, but still you'd stick to energy weapons because of the cost.
One sort of "space" game that comes to my mind is Descent, where the energy didn't regenerate, but had to be collected like typical FPS ammo.
I'd say that in-mission reloads would be a good idea for R2. You could touch down in the flightpod, get rearmed, perhaps slightly patched up and take off again. This would allow much longer and more intense missions which would normally cause you to run out of ammo. Also, remember that a combat landing and rearming takes you out of battle for a while, so this wouldn't be a game breaker.
I'd be a fan of something like that. If you take a two-three minute time out in the middle of a mission, you're running a pretty good risk of some raiders showing up and blasting your battlestar out of existence while you're sitting in the hangar twiddling your thumbs. It seems like a pretty good tradeoff to give to a player - do I get greedy with missile-requiring objectives or do I stick it out and shoot down raiders?
Basically, that was my idea for reloads. Reloads would be paired with a rather hectic pounding by Heavy Raiders and Basestars, so you'd have to time them right, or trade off some of your Battlestar's health in order to get rearmed. Coupled with global missile load tracking (limiting cannon ammo like that could be a bit overkill), this could really help the atmosphere and add depth to the game. Since the only missiles that are mission critical are anti-ship, these could be issued on a per-mission basis, and maybe you could get to keep the spares to use in case of being in a tight spot later. AA missiles would be issued at the start to use at your discretion, and you'd be able to get some more in certain missions, usually by saving a cargo vessel.