I played 2 games of this mode, and when we were playing zombies the top vanquisher on our team was indeed a Scientist. It was a fast match and I thought I had done well as All Star to get 11 vanquishes, but our Scientist had a whopping 21.
I agree that Scientist is more deadly than Engineer. I have always thought that Engineer by himself if a nuisance, but not OP. A mob of Engineers can be a real hinderance though. I remember one disastrous match where our team couldn't leave the spawn point due to being locked down by a team of Engineers (pre-patch).
I don't feel like Scientists make my life miserable in the same way that pre-patch Super Brainz could, but there is little doubt that he often tops the podium. However I think the game is fairly balanced currently, in terms of plants vs. zombies, and I think that whether playing plants of zombies the better team will tend to win. For example we may have crushed 3:0 in the Gnome Bomb match I mentioned earlier, but when we played plants we also won 3:0, and it was an all-plants podium.
Also, great observation @spIash_damage about people not complaining about the OP characters they play themselves. I tend to ignore "SO AND SO NEEDS A NERF!!!" threads, since usually they are just people venting their frustration about a character they haven't figured out how to counter yet.
I have noticed a lot of murmuring about Scientist, though. I think that as people figure out how to play the character well, he's getting more deadly.
All that said, in the hands of a good player, any character can dominate a match. I played a bunch of games with an amazingly good player recently. Full lobbies in Boss Team Vanquish, and this player was vanquish master for about 10 matches straight. Rose, Cactus, Deadbeard, All Star, whatever. And this player's team won every single match, too. It made me rethink some of my ideas about certain characters.