I like respawning enemies, and I like them to be fun and a bit of a challenge. I have no problem with stopping and fighting a medium difficulty enemy every now and then (like the Sheegoth infants or Space Pirates in Metroid Prime; perfect respawn enemies, and MP2 lacked such fun respawns). It's a fun release from backtracking and keeps the game interesting.
I think respawning could be done better, with more variety (like limited randomness, like Ian suggested). That would be very cool, to not know exactly what's waiting for you.
And for Ian, most of the time the enemies in MP2 are very easy as far as respawning goes, but some enemies do prove a problem. No real spoiler here, just telling you what two enemies bothered me the most in the game:
First off, the MP2 equivalent of the MP1 Sheegoths. I forget the name, but they're in Torvus Bog. They're much harder to kill than Sheegoth's were (one super missile to knock the back off and a charge shot or two to kill them after that) and are stronger and quicker, and you have less room to fight them. Those aren'ta big deal if you have missiles, though, which you probably will. What I hate are Dark Space Pirate Commandos, who are basically Chozo Ghosts x 5. Very hard, probably about five super missiles to kill them, and you can only see them with the dark visor. They leave if you don't beat them in a certain time limit (And if you kill one it stays dead next to you fight), but they stay dead once you beat them in that time limit. Only one or two areas have them permanently.
Zelda respawns are good, too, because they're fun to fight without being a problem or annoyance. Same goes for games like Mario, and though upgrades are rare in Mario, you're used to killing them by then, so it's no problem.