This episode doesn't really feel that long; I think that's b/c the plot would be really suitable for one of the Pikachu shorts they used to show with the movies (or maybe still show and I'm just not aware of it). It's a pretty fun episode that's not to be taken too seriously. The way Deoxys is able to recover right at the time TR attacks is too coincidental (as well as ensuing demonstration of all its abilities), but other than that, there isn't anything too eyebrow raising (well, come to think of it, the way Staravia's wing attack breaks TR's golden arm thing and then Buizel uses Water Gun to make it explode is kind of weird; if it were that easy to take down, Pikachu and Piplup should have been able to take care of themselves). I liked the small element of mystery about who the pokemon is that's maintained for much of the episode; it's a way to keep your interest. And it seems like that's what the writers were going for, based on Dawn's comment at the end about the mysterious pokemon there are in the world.
My favorite gag in this episode is actually the way Buizel is able to pull Ash around with no problem, but Piplup is absolutely drained after rescuing Pikachu and swimming to the island. Obviously, the contest that starts the storm (and does the group no bit of good at all; seems like Pikachu isn't aware of just how far away the pokemon are from the boat, since Ash and group don't even give storm a glance, unlike what Pikachu envisions with the lightning being pretty obvious) is pretty fun. I think this episode is probably the best of the ones focusing just on Pikachu and Piplup, in terms of humor. There's another one that's pretty memorable (focuses more on Piplup, but you really get to see who Piplup cares for, which sets up nicely for the final episode of Sinnoh), but that has a pretty serious nature. So I think that makes this episode the best for pure humor.
My favorite scene in this episode is a pretty subtle one. It occurs when Deoxys is leaving. Pikachu, Piplup, and the other pokemon there are waving goodbye (and presumably saying it), but Ash, Dawn, and Brock are not. I think that's an awesome, awesome touch. This episode wasn't about them really, and helping Deoxys wasn't their adventure. They smile in appreciation of what's going on, but they're just observing, while Pikachu and Piplup are the ones who were really invested in Deoxy's recovery and would really be the ones emotionally invested to say goodbye. It's an appreciation that every good, exciting story isn't always your story. Ash, Dawn, and Brock are sincere enough to know that; but that doesn't mean they can't appreciate and be happy for Pikachu and Piplup, who are both really proud of what they did. That's what caring for someone really means, in my opinion.
Have to say, as a little postscript, that I think this is one of TR's better gags. The fact that they try to fool Pikachu and Piplup (and have already discarded the disguises once our heroes find them) emphasizes that these two pokemon are the characters we're going to be focusing on in this episode (not that this is unique to this episode; I know it's been done in the Riverboat episode, and probably a few others, I'd imagine-I'm complimenting more the gag).