So far for us, we have issues 1, 2, 4 and 5. (Raph, Mikey, April and Leo.)
#3 (Don) didn't ship yet and the movie version itself has not yet shipped.
When we get them, just tack the comments onto this thread.
If you don't want spoilers, then don't read any further!
I think the biggest surprise for me on these is movie 4 was supposedly picking up from the chronology of the other movies, but then there's a twist I'm still wrapping my mind around.
Based on Splinter's trophy room, with the time sceptre and the samurai armor suits (which they didn't actually come back wearing in the 3rd movie so how did they get those?), that implies movie 3 counts in additon to the first movie. I'm guessing movie 2 still counts?? I know there's been interviews with Kevin Munroe and such that discuss how the second and third movies do or don't count in the chronology for 4...guess I'd have to go back and study that stuff again?
But then the prequel comics as a whole present things that came from the Mirage and the new 4Kids cartoon series.
In addition to Karai in the new movie, there's fights with Triceratons in the comics, the Utroms are mentioned, and Leo knows about the Ancient One. So it's placing that stuff in with the movie chronology that's what I'm working through.
So during the time after the movies, they get involved in these other things like the Triceratons. And something with the Utroms that isn't shown in the comics.
Splinter had them cut off from being involved in "the world of men". So they were strictly dealing with alien presences, not anything like Foot ninja, either. Does this support that Leo (and the others) do not know who Karai is until they see her working with the Foot in the 4th movie?
(As mentioned in my movie review comments, I'm not clear on the movie whether Leo did or did not know who Karai was when she attacked him. Due to dialogue changes from the novel, where the novel clearly states Leo doesn't know who she is. But the novel should be discussed in a separate thread. 
)
There's certainly some character adjustments from where the movies left off, in what I would say are more maturing kinds of changes. Leo was clearly taking on more of a leadership role than seen in the 3 movies.
Don and Mikey started thinking about jobs leading to earning money. (Which I really like as an idea in general that makes sense!) Naturally Mikey's job involves kids, I'll be looking forward to seeing the Don issue when it comes out, hopefully has something about his starting on the tech support stuff.
Although in the Mikey issue when Mike ends up out on the hockey ice rink--"ice ice baby"
Aaaaah! Of course, then he says he hates that song.
But Mikey still wants to be a hero, despite Splinter's orders. For the "greater good". And starts on his Nightwatcher fan kick, which I think was a good bit of fun in the movie, too. It's like he's living out his desire he's denied having through his fandom--which is an interesting turn on the RL fandom, eh?
And it was great to see a Mikey and Don team up for the Cowabunga Carl gig, that doesn't get shown in the movie, although we had seen something of Don working with Mikey in the early movie clips at SanDCon last year. (Hope it's on the dvd!) Obviously Splinter appreciates the cake.
Raph gets upset about criminals preying on people, and being denied helping them. And probably the extra push from being jealous about Leo being sent out for the training, on top of once he meets up with David it's the phone call to see Leo off that messes up Raph from having any chance of saving David from the gunmen. Not that that last part is actually stated in the comic, buuut....
April has quite the adventure getting that 4th general statue! And it set up her transition from I guess, the tv news reporter of the early movies to antique shop seller then using her aquired martial arts skills, too? I'm guessing she set up a new store after the original burned down in the first movie? I noticed the set up on the store in the comic seemed more similar to the new cartoon than the first movie, although the comic seems to imply her and Casey's apartment is a separate location from the store, not just above it like the cartoon. Hm, have to study that apartment thing in the movie too, sometime, just for fun.
When Leo faces the Ancient One, with a reference to the Ninja Tribunal there, I do have the impression this is his first encounter with him. Based on the way the comments are said, it doesn't seem Leo was familiar with the Ancient One's commentary style of "kumquats".
I did like the way the Leo issue ended, the discussion about community and family was very nice. Not a pie in the sky view about world peace/community, but a realistic one about how many people do treat each other. But instead of giving up hope, focusing on the personal and going outward from there.
Lots of fun things to think about, it certainly deepens the character arcs for the movie versions.
I'm glad Mirage did the prequel comics.
