1. I dunno if it's under his control, but my guess would be that it's like a more perfect Kagebunshin, which works on its own until it's dispelled or dies. A kagebunshin after all is also a perfect replica, except that it disappears upon taking a hit.
2. First of all chakra is created when stamina and spiritual energy are fused, so you can't tell a shinobi's chakra levels just by sensing it, if they haven't MADE any chakra yet. Early on we learn it's a waste to make so much chakra unless you're going to use it for anything other than showing off. So Zetsu just has to make a copy with regular chakra levels.
3. I'd say he can probably make clones of dead people, but the clones he makes are weak as well, seeing as how the Kisame clone was taken out pretty easily. My problem is that if Zetsu could make a clone that could at least hold its own against Killerbee for so long, why'd they have to make Pain use his cloning technique earlier to make Itachi and Kisame clones, which required sacrifices?
I actually think Kishi did plan it out in advance, just that it wasn't thought out well. He probably knew he wanted to bring Kisame back, he wanted the plot to go that way, he just couldn't come up with a real tight explanation, hence the Zetsu thing. I mean, he gave Kisame a very different kind of 'death' than everyone else, who had at least some sort of buildup. Plus Kisame's a much more prominent character than, say, Hidan or Kakuzu, yet he was 'killed' off almost as an afterthought. So him coming back makes sense.