A major downfall of Hoenn was Emerald being released. If it never got released, we may have had seen a better Team Magma/Aqua arc, seeing as how Wallace was orginally planned for the show, and Steven made an early appearence. But when the whole Groudon vs. Kyogre episodes came out in Japan, I was shocked to see no Steven, no Wallace, and I was also frustrated to see that Mt. Pyre didn't get any screentime, that would've beaten the crap episodes we got before Groudon vs. Kyogre, hell, we got Lance, something the writers handled mostly poorly. Though, I do believe the Sinnoh saga will be handled properly as for as the criminal organization goes, because there is one team, trying to obtain 2 Pokemon (anime, not games), as opposed to 2 teams obtaining one Pokemon each, writers were actually doing pretty well in the first 60 or so episodes of Hoenn with that idea, but then they slacked off somewhere, probably the Brody episode... Unlike in D/P, where they probably have most non-filler episode plots written and stored away somewhere in OLM Studios. =/
Cyrus probably has a big debut coming up, or before he makes his full appearence to Ash and co., he'll get cameos and small screentime foreshadowing coming events... oh the possibilities.