Aw, I hope this isn't too old for you! I haven't made a site or anything before so I'll try to approach your issue from what's written and hope I don't come across as too naive, haha.
If you're overwhelmed, it might be for several reasons, and a method you could try is something akin to goal-setting. Bullet out what you think are your coolest ideas, anything from mechanics to world-building to character-building options, then scale or organize them by preference. After that, you should try to summarize the principles of your prospective site. A potential mental trap you could be in is having a principle that doesn't align to your ideas – for example, the principle of offering a unique Pokémon site, but the ideas of modded capture threads, gym leader fighters, Lv. 5 starter(s), etc. You might also have too many ideas competing against one another. It's probably a combination of other things.
Another method if you're overwhelmed: research! The good thing about Pokémon sites is people love them; they have history! Even for dead ones, look through different sites and how they've handled some of your concerns. I recommend this especially for determining whether players should play champions. You can look at the gym leaders of other sites and ask the following questions:
- If gym leaders are available to play, do players app them?
- Are PC gym leaders typically active?
- Do sites with PC gym leaders give them an advantage in anything other than progression, incentivizing them to stay active?
Anyway, this is where my greenness is gonna show with some direct feedback.
I want to say you can have a system that pivots on player-characters if you incentivize players. I love that word. "Incentivize." Anyway: story involvement is a big incentive, probably the biggest; I’m on a site right now where everyone is in the noble class because that’s where the preexisting relationships are. You’re on a good track with the emphasis on families – court drama is spicy – but there’s also a variety of what characters can be, so it could end up being a crap-shoot after all of whether you can find enough champions. Research will probably be your best bet here.
I do think champion-balancing – having members use equal Pokémon – is impossible if everyone is subject to the same progression system. People will be punished for not being as active before the champions grind up and wreck them. That, or you’d have to awkwardly penalize champions or force them to use certain Pokémon for every fight. And this is where Conquest’s mechanics could come in! I’m surprised they weren’t mentioned anywhere. You literally could use an Eevee throughout Conquest’s main story and get away with it if you had your troopers pull up with you because battles are multiple “trainers” on the field at one time. So a player could go AFK but their team would still have people active. It might be more mechanically advanced but there’s a precedent for faction-based roleplays… I don’t know, I think it’d work really well.
Of note, I'm very interested in a roleplay like this since I always have a blast writing Pokemon and Conquest had a lot of potential! Ginchiyo is really hot, I mean I hope I'm not late on this and I pray that some of this is helpful.