Not to toot my own horn, but...
Yeah I'm that shmo who made that Pokémon: Pee Red Version flash two years ago that was sorta popular, a bit. Now I'm not bringing that up because I want to compare mine to yours, or even to draw attention to mine. I'm reviewing this flash because I saw myself in you and since I've made a very similar flash, could offer you advice that I would have appreciated. After all, like me, you actually respond to your reviews, which shows that you do care a lot about what you're putting out there for people to see. And what's more, you expect actual criticism from the negative ones, which I applaud you for. Anyway, I've spent entirely too much space with this probably unnecessary intro. On to where this flash actually gains and loses points in my book:
What I enjoyed most was how you set up a cast of characters with personalities. I actually wanted to see what was happening to Ash and Gary since they had a bit of chemistry together, and giving them both a team of unique Pokémon kind of separated them from the other variations of them we've seen in countless flash movies and Nuzlocke fan comics. Prof. Oak's voice is great. Oak being a pervert is nothing we haven't seen before *ahem*, but the way that his voice actor got it down was very enjoyable.
The sprite work was very lively. The way the camera and backgrounds were tweaked to make it seem like we could see all around the characters (Ash's room) was nice, and using the trainer sprites for close-up shots was a nice touch. The lip sync carried over to when they were small, and the characters bounced around and moved like they were actually emoting, which is a bit more than you can say for my old version. But even if the animation does kick the ass out of mine, it isn't perfect. There are a lot of small hiccups that make you wonder why they're even there, some sounds were off or missing all together, and the subtitles seemed stretched at times and were riddled with spelling mistakes, which drags the presentation down all together.
But all these things I'm saying don't seem to be enough to drag the score down to a 6, and that brings me to this flash's biggest problem: its sense of humour. I see how you've been hearing this a lot, but not everything has to be about sex. Hell, sometimes there are times where you don't even need a joke. Having no joke actually IS better than having a bad joke. Case in point: bringing up the Water Temple just to make a TWSS joke about it being (*tee-hee*) HARD. While 3% of your audience may laugh at That's What She Said jokes, the other 97% will be either cringing or facepalming. It seems like a lot of the jokes were thrown in like that. Another good (or bad, really) example is when the nerd approaches Ash and Gary and says that Cynthia is cute, but is only into girls, because apparently just bringing up lesbianism counts for a joke (and we find out later that that isn't true, so this anti-joke doesn't even have a reason to exist). Immediately after, he gets kicked in the balls. Wait, why? What promted Ash to do that? It just seems like you didn't put much thought into what went there. Also try to deliver a joke and not just point it out, like Prof. Birch wearing sandals. You can't just have him say "how gay is that?!" It's lazy and embarassing, and it set the bar low for the rest of the flash.
Holy crap am I ever running out of space. Let it be known that while your humour isn't to my liking, there was enough that I liked that stopped it from being a total stinker. Or even kept it from being bad at all, a 6 is above average. I laughed out loud at the line "WOAH, was that me?!" The ending especially I really liked. The Star Wars joke didn't seem totally forced; it gave me a chuckle. I have no idea why you're catching so much flack for the Sandshrew fight scene, I thought it was the best part of the flash. It's probably one of the best use of sprites that I've seen, not to mention funny, too.
In conclusion, it had its moments, and I believe you will get better in time and learn from your mistakes.
PS PoopBrown was too obvious a title choice.