So I loved the first Batman Crossover with TMNT and just bought the sequel and something I'd love to see would be for TMNT to join the DC comics universe I think they'd fit very well and I'd like to see mutagen get used by various villains and see the potential insanity it could wreak on the DC comics universe. I'd also like to see the Shredder and Krang mix it up with some DC heroes.
One way I could see them doing it would be for a sort of disaster to occur that causes the turtles reality to merge with Batman's reality permanently. Which I think would make for a good story arc to.