JJ Trek is "The Amazing Spiderman", "Fantastic Four", and "X-Men".
We'd all like to see some crossover in the Marvel Cinematic Universe (because it's a common theme with so many of the heroes based in NYC), but the problem is Marvel has the rights to The Avengers, while Sony holds the rights to Spidey, F4 and X-Men.
So, you are very unlikely to see "New Avengers" made by Marvel for the silver screen because you can't get Spidey and Wolverine without paying Sony a hefty sum of your profits. You wont see the Avengers hanging out with Reed Richards and crew either, because again, you'd have to pay away all your profits just to make it happen.
And the fans are the ones that lose out.
That pretty much sums it up. Well, except for minor details (To my knowledge, Sony owns Spidey and Ghost Rider, Fox has F4, X-Men, and...Daredevil, I believe) but that's really beside the point, it boils down to JJTrek and STO will (most likely) never ever meet.