If it's crap ... We'll tell you
First off, Michael Bay isn’t directing or writing, he’s the producer on the project, I don’t know why everyone’s acting like Michael bay is the one directing(aka thinking it’s gonna be like Transformers 4 with Turtles). So with that out of the way, the guy who is up to actually direct(John Leibseman, director of Battle LA) and the guys(Josh Appelbaum & Andre Nemec , writers and producers of M:I4) up to write are actually pretty competent in their works, and thus it might actually be good, especially since the writers and director are good at Team based action films. But on to the issue at hand, Michael announced that they’re going to have an alien origin much to the outcry of some fans, myself excluded. Peter Laird, the Co-creator has actually saying if done right this could(keyword) be the best and MOST ORIGINAL thing with the series that has come across his table since the inception of the series. Now, I’m going to use solely things that have been introduced into TMNT(Original comics till the upcoming Nick series) lore already to build you why this could work out better than first believed.
Let’s start off simple, the Idea of them being aliens, throughout the iterations of the animated series and comics, the turtles met plenty of aliens, some that were identified to be just like a turtles (like the Super Turtles from the 87 series). So to introduce the element that they may be from another planet, galaxy or possibly universe, maybe even the future, (as anything foreign to you, can be referred to as an alien) isn’t totally farfetched. The argument I’ve heard is that they’re neither longer mutants nor Turtles; it’s possible they may be a mutation of their people into something unnatural for them, explaining their very limited superhuman strength (picking up foot clan ninjas), and agility(they’ve been shown to “out ninja” ninjas at times) that they’ve displayed at times. Then they may self identify themselves as a variation a MUTATION if you will, of the Turtle.
Now on to why the alien origin might work as a story element, back in the Mirage Comics days of TMNT they made the Utrom, a race of cute pink blobs (I think that’s what inspired the Hanar in Mass Effect), who were in fact responsible ( in that universe) for the mutagen that spilled and gave us our heroes. In the 2003 series, they’ve actually made shredder into a violent (a very uncommon thing for them) Utrom, Ch’rell who used shell body like Krang(he’s not an Utrom but his appearance is obliviously based on it) did in the 87 show, except Ch’rell’s is better and actually human looking, to become the man known as Oroku Saki, who would later become the shredder, named after a Japanese folk tale he heard.
With all that in mind, it’s easy to set up a story, that fits both in the alien origins and keep true to the name of TMNT, hell take my idea:
-Ch’rell/Shedder is a ruthless space warlord, who conquers colonies, then experiments on and tortures their survivors till they join him or die.
-Splinter, after an attack on his homeland that killed his master, with a small unit attacks Ch’rell on his flagship, the Technodrome.
-They have a fight, where they end up crashing on earth after the pilot is killed during an FLT jump, the fight and resulting crash nearly fatally wounding Splinter,but his desire for revenge drives him on to find his enemy.Just as Splinter gives up his searching the wrecked Technodrome for Ch’rell, he finds 4 baby turtle humanoids from a colony Ch’rell attacked, trapped in pods and decides to save them.
-The mutation part comes in here, from them being test subjects of Ch’rell as infants, thus giving them improved physical development, in terms of agility and strength then most people of their race.
-He raise them in the sewers of earth, teaching them what is their near equalivant to our ninjitsu, improving training and weapons from historical records of ninjas on our earth to take revenge, not only for his master but also, their home as well.
-Over the years they train, Ch’rell has kept himself disguised and becomes the publicly respectable businessman, Oroku Saki, but is known in the underground as the ruthless crime boss and leader of the foot clan, The Shredder.
-The Foot clan is an already existing Yakuza styled crime syndicate, that Shredder took over a few years before, making there be vocal older members who dislike his ideals.
-All of that leads into of course April O’Neil trying to find the connection between Saki and the Shredder, thus one day running into the turtles, after hearing reports of vigilantes “dressed” like turtles,all the while Casey Jones trying to bust the Shredder’s operations his way.
-Shredder is experimenting on local wildlife and humans (so you can have shout-outs to things like Bebop and Rocksteady) as well as rebuilding the Technodrome all for the old villain motivation of "TRYING TO TAKE OVER THE WORLD!".
If I can come up with this just by looking at the elements set out and mauling over it for an hour, I don’t know how the writers of M:I4 can’t come up with something better over the course of a month or two even a full day. Now it’s been officially confirmed both creators Eastman and Laird are actually completely on board with this idea as well, with Eastman on studio grounds and talking with Leibsman and both writers, as well as Bay. This might not be as bad as you may believe just because Michael Bay’s producer and they’re changing things.
Oh and I just thought of something, them being aliens, with different taste then humanity, gives them a reason to buy those weird pizzas with stuff like Marshmallows, Chili Peppers and BBQ sauce together on a slice like the old show.