One of the biggest annoyances of my youth was that the transformers cartoon was a different continuity from the comic; despite both being put out at the same time.  (I was young at the time, so it's a good thing I didn't know Ironhide's toy didn't have a fricking head like the character does in both media). 
 
What would you think of a Marvel ongoing cartoon that was in-continuity with the comic? 
 
For starters, it probably wouldn't star a main character by himself.  We can't have Spiderman:  The TV series that takes place during the year 2012 (for argument), while having a comic book go alongside.  Why?  Because the tv show would be constantly playing catchup and neither would be able to have much change. 
 
HOWEVER, I think it'd be possible to do a team book - especially a team book with relatively history-free characters.   For example, imagine if Professor X takes the Young X-men back east in the comics.  We could easily see a tv show (~12 episodes) featuring him, and a select cast, teaching these students and having them do stuff.  A companion comic can deal with comic-continuity stuff, while also refering to things that happened in the show.  To read "New New Young X-men #1", you'd need to watch episodes 1-3 (the origin movie).  Of course, maybe the book could contain a link to the episodes online w/ a special key.  Or something. 
 
A better option would be to explore a more "fluid" character - like Deadpool (but NOT Deadpool) - have the tv series start someplace, tell a nice story that's in continuity, but not continuity-burdened, and gets people interested.  Later they pick up the ongoing comic, and see things from the cartoon referenced. 
 
So... who would be the best character to do this with?  I think Firestar.  Her comic-book history is rather dense, but it should be relatively easy to ignore all of that - both on tv, and in the comic.  Give her a personal life, have her interact with New York super heroes on occasion, and MAYBE give her a "team" (Young allies... eh) of super heroes to hang around with on occasion.  In the "companion" ongoing comic book, you can deal with more "adult" themes occasionally (Cancer?, drugs, sex, abuse), do the occasional necessary event-crossover, and have her deal with elements of her past that were touched on, but not delved into, on screen. 
 
Other characters that this could work with are Captain Britain, Blade, Wolverine (bloody, bloody wolverine), X-23?, Gambit, Kitty, Moon Knight, Daredevil, Nova, etc. 
 
For this to work, it should NOT be "dirrectly tied into" the tv series, but there should be significant efforts to refer to things from the tv show in the comics, and the writers for the comic should be involved with the show and visa versa. 
 
It strikes me that this kind of series might lead to higher comic book sales.  And a more fulfilled audience.