Shepard has the rep of reaper killer, wether or not he actually hands on throttled soverign himself is irrelevent.
His reputation as a reaper killer has earned the unwanted affections of the reapers themselves. Shepard is the only person Harbringer addresses by name directly. The reapers know of shepards reputation, and while they know the little fleshly being can't beat up a space ship with his bare hands, they do have reason to want to go after him..... Hell they wanted to buy shep's body from the shadow broker...
The dialouge throughout the game makes it clear and evident that the collectors under harbringers directions are targeting shepard himself.
The role shepard plays in the game is that as TIM's bait... Shepard dosn't know he's bait.
Are the collectors playing TIM or is TIM playing the collectors.... again I refrence the name.... The ILLUSIVE man.
There are indeed a lot of questions left unanswered from ME2, but that's because it's the "middle" of an epic....though ME1 did have its own story resolution so did star wars a new hope...... the empire strikes back was the middle leaving lots of unanswerd questions .....
I think when ME3 comes out , you'll see exactly what ME2 was all about.... don't expect it to stand alone as a story , it's not a stand alone story ...its the middle chapter which throws up all the questions for you.
I believe we'll find that TIM is serious bussiness in part 3.
Back to the topic of the thread....I doubt all the characters will return for the final chapter.
My guesses on who's gone.
I think Thane is a goner because of his condition.
I think mordin is a goner because of the short salerian life span.... he might be "too old" come part 3.
I think Jack is a goner because she is wreckless.
Zaeed and Kasumi, awesome characters both, but really just DLC..... so , yeah not supported.
Who Stays..
Garrus and Tali are pretty much gauranteed to stay , as you don't have them for two episodes only.
Ashley and Kaiden.....will be at the expense of Miranda or Jacob, as honestly they are all as entertaining as watching paint dry.... and all four of them available to play would be dullsville, but shep does need a human love interest.
You need your token krogen... so grunt is likely to return but not wrex as he's too busy..
You need your token asari , samara has her code, morinth can't be trusted, i reckon its liria again though as new shadowbroker ...unlikely, though why she became intell after a life of archeology is beyond me....
So new characters are likely to be those who fill the unfilled class.... you'll need an infiltrator if thane and kasumi are gone..... garrus remains soilder, tali remains engineer... so who's left on the class wheel to fill?
hell maybe the idea of ME2 was to give you a list of "scum" like team mates... so when ME3 comes along.... and you are paragon or renegade.... you can chose nice shiney allience bores...or scum of the galaxy / disgraced team mates.... as I'm sure ME3 is going to make you chose Allience or Scum..