So the thunderbolts provide an excellent concept: villains in the guise of heroes or, villains freed from moral / ethical restrictions. Its either a redemption story or a Marvel cross between Big Brother, Smokin' Aces, The Avengers, and a dash of HBO stand up humor.... When Dark Reign ends, will we see another make shift team awkwardly assume the role? Or could there be another way to REALLY make this team fun to follow?
 
First of all, roster switches.. Its a Thunderbolts tradition right? Something to consider is where are the Dark Avengers going after Osborn breaks down? Do they get their old spot back? Will  they still follow ol' Normy?   I hope not. I hope he takes the H.A.M.M.E.R base and declares it a haven for The Hood's syndicate, ruling it as the armored Grand Goblin (Green Goblin in Extremis) with Menace by his side. I'd imagine by then the disassembled Dark Avengers and Thunderbolts will be tired of following his lead. 
 
This opens up the avenue for a merger of sorts.. combine the aspect of both Thunderbolts teams.. An Anti-establishment Black Ops team of assassins for hire who will either kill or simply 'bounty hunt' super villains... or heroes... provided the money is right and there's a justifiable reason (even if its slim).
 
I'm not fan of Mister X, Paladin, or Scourge/Nuke. They make great supporting characters in story lines but, on a team? Come on. They should be replaced with more popular characters who have hero/villan/ethical conflicts, conflicting personal relationships, and a workable darker sense of humor.
 
As such, I'd replace Mister X with Deadpool, Paladin with Bullseye, and Nuke with Task Master. They all have assassin for hire qualities and interesting relationships as friends or rivals. Plus, Deadpool and Black Widow II have that unspoken 'thing' based on the competition between him and Task Master to pick her up. You keep Ghost, Ant-man, and even Headsman (he adds a violent element and could be tutored by Task Master). 
 
Also, you change up Venom. Gargan sucks as Venom though, the animalistic tendencies of the symbiote are fun. I'd like to see Arachne as Venom for awhile. Hot one minute, monsterously vicious the next.. and shes got a touch of the hero/villan conflict going on herself. It'd be interesting to pair her up with Ant-man. Have him maneuver her into bed and then 'not call' or blow her off... Leading to Arachne and the symbiote (now influenced by a female host) developing an obsessive attraction to him as a subservient mate lol.. Kinda play on that whole 'crazy girl won't let me leave' humor and give ol' Eric his just deserts for playing the ladies. 
 
Finally, just for that 'you need a super strong character to be taken seriously as a team' thing, why not have the new Thunderbolts recruit Juggernaut? He's not doing anything and is conflicted between the hero/villan lifestyle. After all, even if he beats up, kills, or robs villains... he's still beating people, murdering them, and stealing their stuff. Evil enough for Cytorak maybe? :D
 
The final roster stands as:
 
Black Widow
Ant-man
Ghost
Deadpool
Task Master
Venom (Arachne)
Bullseye
Headsman
Juggernaut
 
By every sense of the term, they become the Anti-Avengers: Similar powers but, opposite approach, motivation, mentality, priority, and methods of operation. Also, they have links to prior conflicting relationships with teams like the X-men and X-force (HA, X-force vs THIS Thunderbolts.... hmmm), :D

I don't think there'll be too many significant changes until the end of Siege.

By the end of Dark Reign, its very possible that there will be no Dark Avengers or Thunderbolts. It is also possible that Ares and Sentry will be in a team that is probably a reincarnation of the Thunderbolts. But what would make sense about the Thunderbolts future, is that Baron Zemo may return

I believe the Baron Zemo makes his return in 2010

Bring back Penance!

Zemo hmmm? Thats interesting I suppose. I really liked this  chaotic black ops squad. I thought the new direction so far was interesting. I do agree though that I miss Penance.

My guess, the Thunderbolts will go back to being about redemption.
Songbird, Mach V, and Fixer are all definite to return.
Radioactive Man also likely.
Parker mentioned that only one of the current team will carry over, so my guess is Paladin cause 1. Against killing 2. Worked with Cap, 3. Feels guilty being under Osborn 4. Ant-Man is gonna run for it.
Last spots are iffy, but my bet is on either Constrictor or Diamondback from the Initiative right now.  Constrictor is very much trying to redeem himself for his prior actions.  Diamondback will have to redeem her image for being there when Thor was taken down, and she would also be the second female on the team.  Of course, they either or both of them needs to survive Siege, which is looking bleak.
Round off with some surprise choices, and you got the new Thunderbolts team.