It's probably well known by now that FFVII isn't one of my favourite entries in the series, but some of this has to do with the fact that Square keeps messing with it and screwing it up further. The original game had a lovely amount of ambiguity that ultimately left the player uncertain of what really happened and whom to trust as a source of information. While some elements of the game's plot were cleared up by the end, large parts of it were not and it's left to the player to determine what really happened. Every time Square adds to it, with Ultimanias or sequels or prequels or whatever else, they take a bit of this ambiguity away, depriving the original game of one of its strengths and, for that matter, directly contradicting one of the themes of the original game.
My actual preference for whether Jenova or Sephiroth were in control would have been for them to leave it ambiguous, as it was in the original game. However, if forced to choose between having the game explicitly depict one or the other, I think having Jenova in control would have been marginally more interesting. I agree completely with Wolf that Sephiroth is a rather boring antagonist.
This kind of thing just makes me glad they haven't ruined FFVI with pointless sequels and other crap.