I'm one of the few who truly belive that it wasn't originally planned for Shredder to be an utrom. It's my belief that the first season was either completed, or near completed, when the decision was made to have the Shredder be an utrom. Here's couple of pieces of evidence that I provide:
- Saki is drinking tea (or something) in the first episode. Why? Does his exosuit enjoy a good cup of tea?
- I believe it was in the episode "Search For Splinter: Part 1" that the head guardian is shocked when he thinks that Shredder is still alive after the Leonardo cut off the utrom exosuit's head. Why would he think that an utrom would be dead from having it's exosuit's head cut off?
And the biggest reason that I don't think that he was supposed to be an utrom: I just don't buy it. Ch'rell is going to spend the whole first season chasing after the turtles, when he should be attacking TCRI? Oh wait, he didn't know that the utroms were hiding there. But April is able to a little internet search and find out that the guy running TCRI is a guy named "Mortu", which coincidently is the name of Ch'rell's enemy. Something isn't adding up here...