Few words from an outsider here, excuse anything that's totally nonsensical.
Skimmed the posts here and the World Tournament idea is really sticking out to me. I think it's a great way to integrate regions in a way that involves real participation. If this section becoming roleplay-esque is an issue then it'd definitely be welcome for people who aren't inclined that way (and fwiw, I think that if this is becoming RPC v2 then that needs to stop). Something that people can directly participate in will hopefully serve to bring about some more activity.
Regarding fakemon, I honestly think that regions which rely on fakemon to make up their Pokémon population are just gonna have to stomach having very limited involvement in a battling tournament or consider adding some usable 'mons. While it's obviously better if things can be all-inclusive, integrating fakemon for only the sake of regions that make heavy use of them is too ambitious - for both yourselves and for the Battle Server Staff - and something is better than nothing. Fakemon is something that's potentially planned down the line, but it's not something that we can put this section on hold for since it's clear that there are pressing activity issues.
I think that the evil organisation idea is really cool too. You guys could get into some really interesting dynamics there - what the organisation's activities in each region are, where their headquarters are based, etc. If you're thinking of going for the canonical Pokémon-esque structure (i.e., find legend get legend control world) then it could be very interesting to imagine how the evil organisation tries to capture and control each of your regions' individual legendaries. My understanding is that there's a limit on how many legends each region can have, so hopefully there won't be too much overlap and each participating region could have its own "subplot" going on. This is something that I definitely think could get some interest going in the interim while the larger issues are addressed, and something that could last much longer if you stick with it.
I think another thing to consider is that there's no 4th wall here. Skimming the replies just now I saw someone mention something about a "pokémon afterlife" or something like that? This is something you guys can make happen, along with pretty much anything else. Each region could have cool sorts of phenomena like that. Hell, if they were interesting enough, maybe you could even get some tourism going for each region's individual and unique features.
What I'm getting at is that the sky's the limit, and I'm getting excited just writing this post (unfortunately I don't have nearly enough time to participate, haha). Things that already exist in Pokémon - particularly, things that you can participate in such as battles - are good to build a base on but don't be afraid to do things that haven't been done yet. When we made this section we wanted to see what you guys can come up with when you're given just the concept of "pokémon" and... pretty much nothing else, haha. Things've been good so far for sure - the actual establishing of regions has been great. Now, you just need to expand them some, make sure that this is something that people can participate in and that people have a reason to check in on their regions every day. This is all about you guys making what you want to see.