As to Tom's comments, in this post, no, he does not answer directly. In past posts he has said outright that the producers have never in a single instance vetoed the judges' decision, EXCEPT for the hair shaving fiasco when they wanted to DQ everybody except for Marcel, and the producers would only let them eliminate Cliff... for obvious reasons.
As to the "clear villain", season one, I agree, absolutely. This was decidedly NOT the case with season two. If you read comments in the blogs, read the polls, read the commentary on the reality TV sites, it's clear that there's a huge split on Marcel. Half seem to think he's evil incarnate while the other half doesn't see what the big deal is and think he's being treated horribly by the rest. Personally, I was rooting for Marcel in the final episode. Yeah, he's kind of an asshat, but Ilan's response to him far outweighed any annoyances Marcel might have provided, in my mind. As far as I'm concerned, the guy who won was the nastiest one of the entire bunch, and I'm far from alone in that assessment. If you don't get that Sam was the runaway favorite (popularity, I mean), then maybe I'm wrong, but I doubt you've read any of the peripheral comments or press on the show. Go to any food or reality TV site and read the commentary about Sam's elimination. There was a clear crowd favorite in season two, and they axed him before the finals.
Just because producers don't veto the judges' decisions doesn't mean they don't have a hand in making them. In my opinion, those blogs aren't all that illuminating, it seems like they are put there to try to convince us of how fair and real the show is. Since when have ratings and money not been the bottom line in reality TV, though? For all I know most of what the judges write could be a lie to try and sell themselves as being 100% honest and ethical, increasing the show's believability. All three Bravo reality game shows have the same formula(they look and feel the same, with the same type of drama between the contestants, and the same general attitude from the judges, also the same elimination ceremonies), so it seems unlikely that the producers would give the Top Chef judges complete freedom in choosing who gets to stay or go. The fact that they kept Michael for soooo long when he obviously sucked made me think they wanted him to stay and fulfill David of last season's roll as a loveable underdog. Unfortunately he sucked too much and it didn't fly. Many of the contestants appeared to fill the character rolls of people from season 1: Sam was Harold, Marcel was Stephen, Betty was Cynthia, Suyae was Andrea, Michael was David/Miguel.
Marcel isn't as hated as Tiffany, but he was clearly the only villain type character this season, and it seems as if the producers tried to show that as much as possible. Several episodes ended with someone threatening to beat him up or yelling at him to "shut the f*ck up" because of his annoyingness. He even said someone at a bar hit him over the head with a beer bottle because of his roll on the show. I personally found Marcel very annoying(he seemed like a wannabe Stephen from season 1, but fake), but didn't quite understand the level of hatred that the rest of the cast seemed to have for him.
It was in my eyes a strange coincidence that they had the most villain like character at the end, same as last season. As Marcel got closer to the end, the judges talked up his skills more and more. The people that were obviously and consistently shown receiving the highest praise for their dishes throughout the show were Cliff, Elan, Elia, and Sam. Marcel might have been as good but they didn't show it as much with him until the end.
Furthermore, have you considered that the reason the finals were comprised of the two in the "big rivalry" is probably because, knowing who the finalists were, the producers spent half the season creating that big rivalry through the editing process? I think you have it backwards. I think it's highly unlikely that they knew Marcel was their big villain and Ilan was his big enemy and they therefore conspired to make them the finalists. I think it's highly likely that, knowing who their finalists were when they went into editing, they creatively cut and selected clips to create or emphasize that rivalry over any of the numerous other personal conflicts that I'm sure went on. You don't think if Sam had made the finals instead, he could have just as easily been portrayed as Marcel's big enemy?
In almost every reality show there is a villain, and it gets them ratings, so it seems obvious that the producers would have had their eye on one for Top Chef from the very beginning. I don't see how they could have not known about the one-sided rivalry with Ilan, when they are constantly interviewing the contestants on how they feel about each other. Betty would have been a more obvious enemy for Marcel in the end, but I don't think her skill level was high or refined enough for them to sell her as a final contestant. Michael moved on ahead of her as the underdog contestant(only room for one).
While Sam was more loved than Ilan, he was also less outspoken about his hatred for Marcel, and people involved in the show have made several comments about his lack of expression. I called it that they were going to keep Ilan and Marcel before the end of that hawaii elimination because those two were the closest thing to a rivalry left of the contestants. The reasoning that Sam didn't technically cook anything and therefore should be eliminated was suspicious sounding to me.
As far as drama, there was a whole lot. Cheating, people quitting, threats, shouting matches, breakdowns, physical fights. This show is made to be entertaining.