These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Songbird is by far the most popular member and has been involved in every incarnation of the Thunderbolts, as a member or not. She is usually the represented member if the Thunderbolts are mentioned, became a playable character in the second Marvel Ultimate Alliance game and quite a few fans even requested that she make the cut for Marvel vs. Capcom 3.
Amusingly, these two breakout characters were chosen by Busiek for opposite reasons: he wanted to use Screaming Mimi because she was a blank slate that he could do anything with, but he wanted Moonstone because she was too well-defined and awesome a character to pass up. While neither is really a mainstream A-list character, the series put both of them on the map.
It Was His Sled: The Thunderbolts were actually the Masters of Evil. Despite this, the initial twist still works.
The Woobie: Troll has her moments, such as the downcast look on her face shortly after getting taunted by other prisoners, or her run-in with past!Songbird, who she hasn't figured out doesn't know her yet.
Broken Base: The general reaction to the announced team was They Changed It, Now It Sucks, but after some time and a new creative many have warmed up to the team. Although a vocal faction still does wish to see a return to the original Villains forced/attempting to do good or more specifically a return of fan favorites like Zemo, Moonstone, Songbird and etc.
Moral Event Horizon: Red Hulk crosses it when he tries to murder Punisher just because he quits and gleefully responds to an enraged Elektra, who finds out about it shortly after, that she can't prove it and should be quite before he kills her too.
Nausea Fuel: Deadpool swimming naked during the Honduras arc.