I'm pretty sure most of us think we have better ideas for a particular episode of TMNT or comic than what the writers would come up with. Either because of some fluke of logic or something just not feeling "right" for the story as a whole.
As an example, I would polish up the Krang Villains Mini. One way or another, he'd have to end up trapped on Morbus and eventually kill his father's arch enemy. But, I'd begin that story a little differently.
Spoiler:
I'd begin it as normal, with Krang learning that Ooze has been stolen and one of the Utroms has died. But rather than Krang rejecting the Rock Soldier informant's help and somehow connecting that with helplessness in his youth, he instead thinks of something different, while still connecting to his young brattiness. And make him a lot younger. Bobby Curnow said he figured he'd be 19 or 20, but I'd make him something along the lines of 14-16; same age as the turtles presently. At least in equivalence.
Instead, he'd connect the death of one Utrom to one that affected him in his youth. Like the murder of a relative - but not the mother because damn it, Bambi Syndrome is all over the place in IDW and it needs to stop.
So, when Quanin arrives to speak with Krang it's to tell his uncle has died on Morbus while trying to subdue Traxus. Krang's mother is with him this time, but maybe she'd only have a few lines; her brother just died after all and she'd be pretty shut down. The young Krang, enraged, demands to go on the next mission to Morbus so he can enact revenge. Of course he's told no on the spot. Not only does he have no military training - being too young to begin it - but he's also too important to lose. (Alternatively, it could be Krang's own older brother who was just killed, and it would be the first time Krang's extended family would be discussed. Shredder's needs some work too but that's for another time)
Then the story continues as normal. He stows away, he gets stranded, he mans up, kills Traxus, and gains his father's respect again. And a text box implying he had one thing to fear on the return home - his mother.
Returning to the present, Krang doesn't kill the Rock Soldier because that's dumb. The soldier he had modified to withstand bullets wouldn't be taken down by his tiny little teeth...or strangled...or whatever Krang did to kill him, it was pretty unclear. He just snaps back to reality and goes to deal with the dead Utrom.
Ideally, the modifications shouldn't change too much in the storyline, just within its own little block and maybe even patch up some plot holes that crop up unintentionally.