And if Team Rocket is anywhere near as active in Johto and Kanto as they were in the early sagas (and there's no reason to believe that they aren't), I would think Lance would have his hands full dealing with them and, I don't know, protecting those regions from the bad guys.
I don't remember him saying anything about why he suddenly appeared in Hoenn except to stop Aqua and Magma (and Groudon and Kyogre) from threatening the stability of the region. He was, in a sense, "just there," while those who actually would've had a reason to be there--Steven (the region's strongest trainer) and Wallace (the guardian of the Cave of Origin)--weren't, for some reason. The point is: Lance had no real reason to be at the climax but was, and Steven and Wallace had every reason to be there but weren't. I think we have every reason to complain about that.
Anyways, to answer the thread question, yes, I do think that they were handled poorly--in the latter half of the region. I said it many, many times, but collectively, they had around six appearances before Lavaridge Town. Okay, that's fine, 'cause the episodes they were in were generally pretty good and we finally had some competent villains who weren't complete pushovers in battle. So, no real problem there. They didn't show up between Ash's battles with Flannery and Norman, but that's to be expected, since they did nothing between those battles in the game. The Weather Institute was also pretty decent, and once again played up Aqua and Magma as being serious threats.
However, this is where the writers seriously dropped the ball. If they'd really tried, we could've had another two episodes about the two Teams before the final confrontation. Even if they decided not to feature their bases or the minor event at Slateport, they should at least have had an episode at Mt. Pyre and maybe another at the Mossdeep Space Center. They really should have stuck the climax right around Sootopolis, given it another episode, and maybe featured the Seafloor Cavern in the process. But, unless you've been living under a rock for the past couple of years, you should know that, well, they didn't. The writers had all of that decent plot-building through the Weather Institute, but they decided to take the easiest possible way out and leave us viewers with one of the biggest copouts and possibly the most rushed scenario in the history of the entire anime.
The only "excuse"--if you can really call it that--that I can think of is that they were so hell-bent on featuring all of the Hoenn pokémon that the stuff that should actually matter to the fans ended up suffering. Really; replace one crappy filler between Fortree and Lilycove with the Mt. Pyre event, remove one less mediocre filler from later on for an extra K/G episode, and replace the Space Center plot with the one from Emerald...it's actually decent writing, which would boost the show's success. Why do such trivial concepts appear to be so goddamn difficult for the writers?
