While I would still favour the Bulls, the more I think about it, the more that I think that Houston would be in with a chance. If my memory serves me correctly, the Bulls had a very poor record against the Rockets and the Spurs, during their championship years of 1991-93. I don't think it is any surprise that these teams had the two best centres in the competition. The Bulls often struggled against teams with quality big men. New York also troubled them in 1992, with Patrick Ewing in the middle, which was a big surprise.
Otis Thorpe was a very good, very strong, and very underrated player. I was shocked when they traded him as I thought thathe was an integral part of their 1994 championship. He played very well in the 1994 finals, had played his entire career in Houston (I think), and, from what I recall, had very respectable numbers. While the trade for Drexler may have produced another championship, I can't help but feel disappointed at the lack of loyalty shown to Thorpe.
As for the Bulls of 1991-93 versus 1996-98, it is very hard to say. In terms of the amount of games won, the latter version was clearly the more dominant team. But, was that because the league was not as strong during that time, or because the Bulls were so good?
While I agree that Jordan played a smarter game after his comeback, I can't help but feel that it was partly out of necessity. Jordan was older, and, as a result,changed the way that he played. He had lost a bit of speed and was not quite as good at driving to the hoop. He became a brilliant post-up player and relied on his jump-shot a lot more. While I think he was, perhaps, just as effective as before, and a better team player, I'd have to say that, if given the choice, I'd take the pre-retirement Jordan. He was unstoppable, still very fast and athletic, and, during the 1993 finals, had started to develop his post-up game. (It's a pity that Jordan did call it quits in 1993, as I think that we missed seeing him at what would have been his most masterful, and complete, time as a player.) I also think that he was as mentally strong in 1992-93 as he was during his comeback.
Pippen is a completely different story. While he had developed into a very good player by 1993, I don't feel like he really flourished until Jordan left. He took his game to a new level in 1994, and developed into one of the game's best players. I have no doubt that, as a result of Jordan's retirement, Pippen was a much more valuable player to the Bulls during their second tenure as NBA champions. He was more confident, more mature, and, definitely, mentally tougher.
When it comes to the power forwards, I'd have to choose Rodman- he was the best rebounder ever. He may have been a liability in offense, but he still got a heap of points, and second chances, off offensive boards. His rebounding at the defensive end also limited the opposition's scoring opportunities. I also thought that Rodman was a good defender. Admittedly, he was not as good as he was during his Detroit days (when some were saying that he was the best one-on-one defender ever, and, certainly, along with Joe Dumars, one of the most effective versus Jordan), but he was still better than Grant. The only thing Grant had over Rodman was scoring, but he wasn't really that good. In fact, if he didn't play for the Bulls, I doubt that he would have gotten the wraps that he did. Don't get me wrong, he was a good, solid player - I just didn't think that he was anything special. In the end, I'd have to say that Rodman's rebounding and defense was a more valuable asset than Grant's superior offensive game.
All in all, I can't really pick a winner. The fairest way to judge them would probably be to take Jordan out of the lineup, and rate the other members of the teams. On that rationale, I may have to go for the 1996-98 Bulls, due to Pippen being an improved player, and me preferring Rodman over Grant. Of course, teamwork would also be a major factor, as would the other players in both teams.