I;m going to go with 1987 version of Shredder only because I like the whole personal level they applied with Shredder and Splinter being once student and teacher. It really makes you wonder what happened between them that made them loath each other so much. Was it mearly that Shredder/Saki was just an asshole? Or was he just ambitous? Or did Splinter do something to cause such animosity to breed in Shredder?
This always facinated me when I was a kid and still does now. Shredder held such spite for Splinter for seemingly no reason. Calling him his sworn enemy and always coming at him with such malice. When seemingly (on the serfice) Splinter did very little to provoke such a a strong reaction. There had to be a cause for it? Just wanting to kill some one just because they hold a postion that you want wouldn't warrent that amount of hatred and passion. Shredder's hatred of Splinter seemed totally personal. And some thing that was never really explored to indepth which is a real shame.
So yeah I like old toon Shredder's origin of being a former student of Yoshi that betrayed and framed him.
The new toon Shredder's origins is interesting but I thought the whole "Shredder is a thousand year old utrom" was kinda just used for shock value (although executed well) that I found kind of meh
, and a bit impersonal.
Not to say that it doesn't make sence in the context of the new toon format I'm just saying I liked the 1987 series take a bit better.