1. Songbird, by a fair bit, but I also like the entire starting 'Masters of Evil' lineup.
2. Busiek.
3. Graviton.
4. The first run, with them functioning as heroes, which I kind of wish ran a little bit longer, and then the 'on the run' arc later. Mostly the first couple years.
5. Ogre, the old 'Factor Three' tinkerer they ran into hiding in an abandoned base in Colorado. Cool callback to a forgotten villain group!
6. I loved the one shot fights with Hawkeye (proving he had what it takes to lead them), Hercules (coming for revenge on Atlas) and Angel (when they tried to steal the old 'Champions-mobile'), but for a group fight, I love the one with the not-really-Avengers. Atlas managing to catch professionals like Spider-Man and Luke Cage off guard (and tossing Cage out into the ocean) showing that he was far more than the dumb muscle his foes (and allies) so often thought of him, Genis-Vell effortlessly punking 'power of a million exploding hyberboles' Mary-Sue by teleporting him away constantly. Great fight. The massive fight between the Thunderbolts and pretty much every other hero under the Purple Man's control was also great!
7. Songbird and Mach V. It being kind of obviously doomed, with her developing so strongly as a character, and him, not quite getting it right, was a good touch. Not every relationship needs to be the soulmates / one true pairing. Some are just not meant to be, but can still be what someone needs, for a short time.
8. Genis-Vell's discombobulation. It was entirely Zemo's fault that he was losing control, and it just burned that Genis was the one who had to be 'put down' for that mistake of Zemo's.
9. Genis-Vell, obviously. Although the group that Graviton burned through like Montezuma's Revenge I would have liked to see more of (Cardinal's daughter, the new Beetle, etc.)
10. Less 'A team' people like Red Hulk, Elektra and / or the Punisher. More people who *aren't* plot-armored against shocking developments or transformations, like the classic team. Part of my love for Songbird is how *amazingly* she was transformed, not just in costume and hairstyle and super-powered role, but also in characterization and development, from Screaming Mimi. That can never happen with Red Hulk or Elektra. It *can* happen with villains like Whirlwind or Man-Killer or pretty much any of the 'forgotten losers' that Scourge killed (not that, in the end, Scourge himself didn't turn out to be a 'forgotten loser'), or even a lower tier hero like White Tiger (whose legacy has gone on to be a great character in her own right!). An X-foe with unexplored potential, like Frenzy / Joanna Cargill, or Carmella Unuscione, or one of the old Alpha/Beta/Gamma/Omega Flighters like Smart Alec or Wild Child or Diamond Lil, or a former Dark Rider like the Inhuman Tusk, could make for a fascinating Thunderbolt. Or Amazing Andy, or Dragon Man! So long as it's a character that can undergo a Screaming Mimi-to-Songbird type transformation, and grow into something new and exciting, in a way that a cast-in-stone character like the Red Hulk (whose sole 'Thunderbolts transformation' seems to be changing his pants) cannot.
Characters that can't change and assume a new identity, or at least reveal some new potential and character beats, like some of the current cast, are, IMO, missing the entire point of the Thunderbolts.