I never was personally bothered knowing the Utrom Shredder was a Utrom. It added a whole layer of dimension to the character of the Shredder. The Tengu Shredder played a great role to it. It added more into the whole backstory of the Ninja Turtles.
Although I never liked the belittling of Utrom Shredder via means by the Tengu. How the Ninja Tribunal viewed him as a joke. Turtles Forever though redeemed this in my opinion. I found that Utrom Shredder is more of threat then the Tengu Shredder in terms of goals and aspirations. I prefer the idea of human Shredder, but the 2k3 series was so great it didn't matter.
The Turtles connection/friction with this Shredder lacked for obvious reasons. The Lost Episodes came on around the time I was 8, and I initially thought the Utrom Shreder was back. I assumed he came back as zombie
It took until Hun dissed Utrom Shredder to figure it out for me.