Ya know... I'm sure the serious stuff would work in this RP... the problem was that it was too consecutive.
Consider the anime. There's the serious [parasitic bomb], then there's downtime with happy-go-lucky times. Just like in the games too; one minute you're just exploring happily and carefree, then you're facing a serious threat with the evil team, then happy adventuring again.
We just need to find the balance.
Like, if there was a break between Fuchsia and Carr, it probably would've been fine, it's just that the serious stuff dragged on too long. We need it in breaks, and to that end Team Skull Flair could easily work as an occasional plot point when we get to Kalos. After all, I'm planning on setting our time there AFTER Team Flare's defeat, so there's plenty of room for a new evil team. And since it would only be in patches, no need for constant involvement. Just jump in when you want to have some short plot, and then leave when we resolve it so it goes back to happy again. No need for a whole separate RP.
That make sense?