Shredder and Krang might be pushovers sometimes, but they're competent villains who try to come up with all sorts of plans in taking over Earth and getting ride of the turtles. The writers just take that in effect. I don't think Shredder and Krang planned on letting the 03 Shredder take over their Technodrome. The writers just made them look weak and silly and let the 03 Shredder be the main villain.
The way I see it is Shredder and Krang could have thrown the 03 Shredder and his daughter in the dimensional portal into Dimension X in the middle of a battle field where Krang's Rock Soldiers are firing. That would be the end of the 03 Shredder and his daughter right there. The writers could have done that and told the audience that those guys don't mess around and know what they're doing.
Shredder and Krang are smarter than they appeared in the special and are smart enough to not let the 03 Shredder take over the Technodrome, despite maybe the 80's Shredder wanting to work together with the 03 Shredder to take over the Earth. As stated throughout the 80's series, Shredder and Krang don't trust anyone including each other.
Again the writers were just using the 80's turtles and villains as punching bags.
Well the way you just put your two cents in, it sounds like you're upset that the 03 Shedder became the main villain, however you also mention that 87 Shedder and Krang could of just put 03 Shedder to an end by putting them in Dimension X, which would of made the 87 Shedder and Krang the main villains, and it seems like you would of had no problem with that. And to be honest, you bringing up Dimension X, well I think you might be over thinking it a bit.
I have to say on a personal note it didn't brother me to see Krang get beat up every now and again. Whether it be from the 87 Shedder, 03 Shedder or Karai, Krang does deserve to get rough up from time to time.
As I stated, I agree that the 80s turtles were made to look foolish at times thoughout the special. But again as Drtooth pointed out in the end the 03 turtles become punching bags to the original Mirage turtles and again the Mirage Shedder was beaten very easily by the 87 and 03 turtles, with a diversion from the Mirage turtles.
I knew the 87 turtles were going to be more "comic relief" characters and I was totally cool with that. The only parts that bummed me out was when they drop their weapons and ran from the Mirage Turtles and when they cried on 03 Raph.
In some ways ryhoyarbie, because you bought up so many points for the 87 turtles and don't seem nearly as upset that the 03 turtles looked pretty lame to the Mirage Turtles, it kind of sounds like you're more of a fan of the 87 series more so than a Ninja Turtles fan in general. I'm not saying that's a bad thing, I'm just saying that's the feeling I'm getting from you.