I already responded to this topic back in the
Turtles Forever thread but I'll restate it here. Shredder was meant to be an Utrom from the beginning, aside from just taking Laird's word for it, practically everyone of the Shredder's season one appearances hinted at a connection between him and the Utroms. Indeed his main goal was to find and hunt down his alien enemies, the turtles just kept getting caught in the crossfire.
Darkness on the Edge of Town: In this the sixth episode of the season one, we see the first hints of Saki's true nature. While sparring with his Foot ninja, Saki is virtually topless save for his abdomen which is conspicuously bandaged. It's also the debut episode for the Sword of Tengu, an artifact of Utrom origin which the Foot uses to recover an Utrom exosuit.
The Way of Invisibility: This episode first introduces us to the Utrom Council and their mysterious.protectors, the Guardians. Both the Guardians and the Council are established as being old foes of the Shredder. Saki also makes his first proactive attack on the turtles, working under the assumption that they are allies of the Utroms. When he discovers they are not, he decides to try and recruit them instead.
The Shredder Strikes: In this episode which features the first real appearance of Oroku Saki in his Shredder persona, he attempts to recruit Leonardo to his cause. Saki claims to be fighting an insidious alien enemy that has infiltrated human society. Although he doesn't explicitly say so, it's clear he's referring to the Utroms.
Notes from The Underground: The plot of this episode revolves around an underground Foot lab, tasked by Saki with excavating a technologically advanced subterranean city. Saki at first believes this to be an Utrom stronghold, when it becomes clear that the city has no connection to the Utroms, Saki terminates the project completely.
Return to New York: Aside from the famous decapitation scene and it's aftermath, this episode also contains the first clue that Saki is older then he looks. Shredder himself tells us that he once used the Sword of Tengu to conquer Japan and give power to the
Tokugawa Clan. The Tokugawa Clan was a real dynasty of Shoguns that ruled Japan during the sixteenth century.
Now whether you think Utrom Shredder was a good idea is an entirely different question and much more subjective. I admit I was a little thrown by it at first, but in time I became quite fond of Ch'rell, psychopathic little Jellyfish that he is. But there can be no doubt that Ch'rell was part of the show runners master plan from the beginning.