Well for starters I'd certainly have Krang come back as an actual threat. If most "aliens attacking Earth" themed movies can battle said aliens for 3/4th of a film, then so can a TMNT. (Rather than spending much of it on a scavenger hunt. Imagine if other alien films did that... say, instead of fighting them, they just have a scavenger hunt to collect pieces of a weapon to destroy them in the last ten minuets of the movie, before they ever actually became a threat.
"Aliens, you just wait there. We'll be back in 80 minutes to finish you.") Also have Krang decide that Shredder is more valuable and an asset to him unfrozen. Although they're going to have to inject Shredder with some of his trademark insanity to even consider helping Krang out after being so rudely frozen and put on a shelf as a collectable.
Alternately... skip all that and do a more Earthbound story that exists prior to Krang and Shredder ever returning. If we need an old foe still then just elevate Karai to head of the Foot in Shredder's absence and let the woman actually DO something and have a big evil plan up her faux leather sleeve. I might prefer this, esp if the Krang/Shredder situation would still be resolved in a 4th.