Let me start off with my opinion on a few common complaints.
Bubbles using Ice Breath: There is no defending that this is a mistake, only Blossom can use ice breath. That being said, it's no big deal. For starters, the power is only used three times during the whole episode and on top of that the freezing factor didn't even come into play, it was all about the idea that they were doing a team attack. It was a continuity error, but it's not a problem.
The Professor's "new" back-story: This also doesn't bother me for the same reason as the above, the show is and always was a comedy. They needed to change the back-story to set up some of the jokes, and so they did that. As someone who watches lots of comedy shows with zero care continuity the fact that they presented a different back-story doesn't do much more then slightly bug me and took zero entertainment away from the episode. Plug in the fact that this episode didn't have the original creators working on it and it is incredibly easy to simply interpret this as non-cannon or a alternate universe.
Now, that aside, let's look at what I thought of the episode as a whole.
It was fucking hilarious. I almost laughed out loud a couple times, which is something I don't do very often. I gotta give the writers props.
The drawing style, which is probably the most controversial thing about the special, was hit or miss for me. They did a good job at animating and some of the scene were actually beautiful. I especially loved the explosion at the end, but a lot of the scenes also didn't look that good to me, but I certainly liked the style more then I expected.
I would have liked it if the opening theme wasn't shortened and they actually bothered to show some of the other villains in the style. They did a good job on what they did do though.
Also, I think I can explain why Mojo Jojo has decayed as a villain so much. In the movie he was a true villain, in the later episodes of the series as well as the specials that we've seen he's a joke. The obvious reason is that, like I said, the show is a comedy, but when you think about all the times they broken his helmet open and hit his brain it's amazing he's as smart as he is. The part where his brain was sort of.... oozing out was also kind of a cool animation.
I liked the episode.