Pokemon Special. Spoilers follow.
TL;DR Version: Although there are a lot of major flaws, the treatment on the whole is probably the best that the series has gotten and, if you're a fan who wants a different look at things, it really is worth a glance.
Red/Blue/Green: Bears most of the burden of world building and does some very good things with it and does some very bad things with it. I generally like the treatment of pokemon training/raising/etc and find the addition of the danger to be a fun and worthwhile addition. The concept of trainers getting down and dirty and having to duke it out point blank is pretty fun. The gestures towards both the anime and the games themselves are fairly cute and, although a lot of them lean towards feeling tacked on, they end up being real fun. Stuff like trade evolutions, in-game references, etc all play out really well.
The cast is fairly solid all around. There isn't a huge amount of depth to anyone, but that's not really what we're looking for here either. There is defintiely enough to allow for some interest in the characters to develop, and the interactions often prove enjoyable. It really helps that Red is fairly charming (unlike his predecessor in Ash). Team Rocket proves to be quite fun as a competent and threatening set of villains, with Giovanni capping it off as an utter badass. The actual plotlines here are a bit muddled, but they generally work out in the end.
I found the fights to be rather enjoyable, involving enough clever tactics and odd stuff to keep you wondering how it was going to go down. Once again, it really was quite the clever choice to have trainers be actively involved in the fights. It is silly stuff, but things like Giovanni's style of releasing his pokemon by kicking the balls just add some fun, over the top action that really benefits the series on the whole.
Where R/B/G really drops the ball is in the world building, though. Considering the importance of gym leaders and the focus on the Pokemon League at the end, the lack of any real explanation as to how they function in the world (as well as how Sabrina, Koga, Surge and Giovanni can go completely rogue without any fallout) leaves an unsatisfying taste in my mouth. I struggle to come up with a real satisfactory answer to a lot of world building questions, and it bugs me. I realize the "Its pokemon, whatever" argument could apply here, but it doesn't change bad storytelling. The world structure really should have been better addressed, dammit. Besides, it would be interesting to see handled well, you know? Unfortunately, this is really only going to get aggravated as the series continues, it seems.
Also, props to managing to stuff most of the pokemon in without it feeling overly forced.
Yellow: One thing I'll give this entire series credit for is using its cast well. Yellow was a cute addition after having a "cameo" back in R/B/G.
Anyhow, this arc felt a lot stronger than R/B/G in general. The villains are better defined and don't raise so many questions if you're willing to overlook differences from the source material. They also, in general, manage to come off as a lot more threatening than Team Rocket. Lance in particular screamed "I am bad-ass, hear me roar!" The Elite 4 also has the advantage of having a much better defined (and respectable) evil plan. Besides, its been a while since eco-terrorism was used as a main plot.
The build up was really hit or miss. Yellow occasionally came off as rather "holier than thou art" but worked as the really kind and nice protagonist type. Bill's screentime was also well used. The city attacks by the E4 were prolly the biggest drag. Potential for really great fights, but the gym leaders on the whole kinda jobbed to the whole deal. It was a real letdown, to be frank. The main cast/team rocket team-ups, on the other hand, were great fun. Silly fights with silly arenas with silly conditions is fantastic and pretty much serves as a highlight of a lot of the things I feel the series does right.
And in retrospect, this bears in R/B/G as well, but Mewtwo is bad-ass.
G/S/C, Ru/Sa, FR/LG and Emerald will be dealt with later.