Would it be possible to make a Breeder cell (used in recharger rifles and pistols) that works as an alternate ammunition for other energy weapons? (the two recharger weapons are rather anemic in terms of damage as it is).

Yes, this works. To do it, set the breeder cell to be the weapon's ammunition, and give the weapon any positive Ammo Regen value. Both of the rechargers use 1 for Ammo Regen, but again, any positive value will work, including floats. The GECK will round floats to the nearest whole number every time you open the weapon's information back up, but as long as you keep resetting that number each time you make changes, it will work. For example, in my http://www.newvegasnexus.com/downloads/file.php?id=37025 I included a unique Recharger Rifle that has Ammo Regen of 0.5. This is the number of seconds it takes to regenerate 1 ammunition, so the Quickcharger Rifle regenerates 2 ammo per second.

By the way, things get a little funny when you try to make weapons regenerate ammunition other than the breeder cells.

i was looking for an alternative to its normal ammo, not an entirely different set of ammo to use in the gun, for instance selecting micro-fusion breeder in the ammo list for a Gauss rifle, and using that as rechargeable ammunition in lieu of regular micro-fusion cells, much like you would use overcharge cells.

That's not possible. The ammo regeneration effect is in the weapon, not the ammo.

There's a formlist called RechargingAmmo or something you need to add them to for it to work right... ish. I think it only accepts 4 types of ammo in it and ignores any more.

It'd be easier to play with the Return Item %ages- MF Cells are set up to return Drained MF Cells at 25% or something, and you can set the item and %age chance to get it per ammo type. So you could easily make your own ammo that returns itself 100% of the time, effectively recharging.

Alternatively the NVSE commands GetPlayerCurrentAmmo and SetPlayerCurrentAmmoCount can be used to fake regeneration.