Having different ammo for each weapon would be good,
this would feel like Quake III.
weapon_lightning - ammo_lightning
weapon_hyperblaster - ammo_cells
weapon_bfg - ammo_bfg
I'd be more inclined to add an ammo type for the BFG instead, seeing as it's such a dominating weapon, and it's very ammo-demanding. Being able to limit or control access to BFG ammo would be more strategically significant and would offer more options for interesting item placement.
That's a good point, from a gameplay perspective. My inclination originally was to change the ammo type for the lightning gun, as the Hyperblaster and BFG have always used the same ammo type (since Quake2). They have similar looking effects, too (and similar looking skins). The lightning gun, on the other hand, is its own beast.. I'm undecided now.