For one, change the title of the next anime saga. Best Wishes just sounds...strange. I like the "BW" reference, but there must be better word combos...!
I was really hoping for the other Sinnoh Frontier Brains to star in the DP anime... It doesn't appear like it will happen, though... The Hoenn Battle Frontier enjoyed a whole season (in a previously visited region, no less), yet the Sinnoh Frontier Brains get no screen time at all! Madness, I say!
Even worse is the fact that they hold a much higher status than all those Characters of the Day in the anime. The Hoenn E4 also missed out, where Sidney, Phoebe, and Glacia weren't featured in the anime...
Come to think of it, I'd like it if all Pokemon League members, rivals, and other important game characters were featured at least once in the anime... All these COTDs irritate me, especially since most of them appear only once in filler episodes. Some of the COTDs are OK, but it just irks me when trivial anime-only, one-time-appearance characters receive more screentime than the game characters.
One thing I would've like is the BW Girl (from the games) appearing in the first and second ep, pwning Ash's Pikachu with one of the Isshu starters, preferably Mijumaru or Tsutaaja. Additionally, I would've liked the BW Boy to take on the "older male" role in the main cast, but still be inexperienced with most of the Pokemon world... But Iris seems promising at first glance (seeing her in anime coloration upped my spirits a bit and rejuvenated my hope for the anime), so I'll still tune in. At the least, BW Boy and Girl should make a cameo in the anime at some point during Ash's travels.
Finally, this is a EXTREMELY long shot (and a "-mon" fanboy's dream), but I'd love a Pokemon-Digimon crossover. I love both franchises, and Digimon is often brought up in comparison to Pokemon during conversations. Palkia could create a tear in space, have Ash and co. travel to Japan for a TV special, meet the Digidestined (the Season 1/2 group, or Season 3), they all end up in the Digital World, have some adventures, back to Japan, a Digimon creates a rip in space (possibly HerculesKabuterimon), a powerful Pokemon and/orDigimon wipes everyone's minds... The day is saved, and canon is preserved and left untouched (for the most part)! :D
EDIT: This just popped up - Ash encountering Missingno. one day on his journey. I know Deoxys sort of resembles it (very loosely), but encountering an actual glitch Pokemon on a random visit to Cinnabar Island would be awesome if it were in the anime.