My vote went for "Team Rocket as a whole". I mean, JJM may not have been evil, but they are the exceptions, not the rule. I mean, Team rocket as a whole did several horrendous things. I mean, they captured and nearly killed a Celebi (4th movie), they were willing to Murder Pokemon (and successfully murdered At LEAST one pokemon), they placed some innocent lives at risk, among other things. In fact, their murdering that Marowak in Lavendar town was the reason why I even HATED that organization. In fact, I think that the reason that Team rocket steals pokemon is so they can kill them.
As for the whole Ash and co thing.
1. most of those incidents were out of self defense.
and
2. they were from a mistaken impression. I mean, since they encountered Team Rocket for quite a while, I can't say that they should have struck first and ask questions later, but they would have every right to be initially suspicious of their actions, since, for all they know, they COULD be up to something.
Besides, as much as i hate to admit it, every character has their flaws, even heroes. I mean, Besides a few people (which of course, might count me as well.), who would want a character with ABSOLUTELY no flaws whatsoever?
the Rocket Trio, JJM, While I do see them as a bit bad, they are not nearly as evil as the rest of the Team Rocket organization (I mean, hey, at least they haven't tried to KILL a pokemon (Maybe they tried to kill Ash, and I am angered that they attempted to do that, but still.).)