There's lots of things I didn't like about those two movies. Episode 1 irritated me more, but it's probably a slightly better movie from the point of view of the series. Both would be alright as stand alone movies... but they're rather poorly written and done in my opinion.
For one, I greatly dislike the massive use of computer graphic technology. It doesn't have the same charm and realism as the old models.
As for Jar Jar, he irritated me immensely, but I do think that he was more or less the way he had to be. It wasn't so much his character as his lines that were insufferable.
Darth Maul was, in my opinion, the WORST villain I've ever seen. We know he's a bad guy, because they told us he was. Other than that, he has no character development whatsoever. Then he dies. I know he's not supposed to be the "main" bad guy, but that was pathetic.
Anikin the boy-hero also bugged me big time. Just because he's supposed to be the pivotal character in the series DOESN'T mean everything has to revolve around him. I can accept the pod racing, though I thought it was entirely too drawn out and overblown. It's the part where he saves the day during the invasion that really irked me.
I think that having Anikin be arrogant and even a bit whiney fit his character for Ep 2, seeing as how he knows how powerful he's supposed to be.
The thing that got me the most was the extremely forced inclusion of C-3PO and R2D2. I'll accept R2 being in Ep 1 as the ship's robot, but mostly just for "fun", not as a serious plot point. And 3PO should have been left out of these two movies all togeather. If they don't have his and R2's memories erased in Ep 3, they just didn't try at all.
Erf. Enough rambling from me.