Mixed...
Mixed feelings about this flash. Considering you are working with Pokemon sprites, they aren't too bad though some smoothing would be nice. There are some moments where the editing is really, really poor almost like there is no real end to a certain scene or shot. Though that only really happened a couple times, otherwise it wasn't bad.
As far as the humour and story; a couple parts were smile worthy, but honestly it isn't my kind of humour. For the most part I didn't really laugh or care about what was going on, the timing was somewhat awkward and I guess I don't find humour in the premise of "Team Feces is turning people brown!" Regardless, it could have done worse with that premise; something like that could sink to *shudder* SeltzerBerg levels. Thankfully, it didn't go that low and while I simply don't think it was funny, I can't say it's bad for the type of humour it is. I think the parts I smiled at were the scenes with Professor Oak, the quick manly "Skitty" voice and the ending regarding the names of the sequel. In fact, that ending bit DID get one laugh out of me - so there you go. It was a bit long though...
One other positive, the voice acting. It was all pretty high quality and while I didn't like all the voices, I can't slight the quality and effort. In fact I'd argue they were probably the most technically sound aspect of this animation.
I guess in the end, I can see why a lot of people like it and it isn't bad for what it is but it isn't my thing. I can see that there was some effort put into it when compared to many other sprite flashes out there, but it simply didn't do much for me - even if I did smile at a few things and chuckle at the end. So for effort, good voice acting, professor Oak and the ending - you get a 6.