As someone who grew up with the original series...
I have to say, even though they did poke a lot of fun at the original '87 series... it was enjoyable to watch them interact with the 2k3 characters, if only to have a laugh at how much 'cool' has changed for me since I was a toddler (I was pretty little in 87 but I did watch it).
I definitely prefer the newer turtles (though I hate that they screwed with the animation after a while on the 2k3 series). It's definitely true that 2k3's Shredder and ninja would obliterate the incompetant 80's villains (let's face it, they were pretty soft as villains go, and not nearly as sinister).
I get that the 80's show's focus was more on the comedy. Fine. But...if you look at the origin of all of it, the 80's show was kind of a butchery of that to begin with, and the 2k3 series is closer to the original comics. They kidified the 80's version, there's no denying that. It worked for me then, but it's good to see it get the jabbing it deserves now that I'm grown.
All of us who grew up in the 80's and early 90's have a soft spot for the original turtles, and I think we've grown enough that we can handle a little fun at the expense of what we once considered cool. We were lame then. Let's face it. We were. I once went out for halloween with a plastic ninja turtle mask and a cardboard shell on my back. Lame. But man, was it fun!
I mean...the 87 show WAS silly. Back then, it was cool. To those of us who were there. But in retrospect...yeah. I'm glad we had it, wouldn't change anything about it, but I'm also glad the property has matured as well.