The Mother Nature thing looks good on paper, but then you realize just how few Plant- and Fey-type creatures there are in the books, especially ones with high CRs. That said, Druids as BBEGs is a good idea. Their versatility is pretty awesome, and since they only need Wisdom and Con you can pretty safely give them a truckload of HP and high defenses.
Honestly thats why I've posted this here as opposed to a dm forum somewhere I know you'll know.
I tried to get away from a top down design but looks like its needed, I'll look for plants and well shoot them down/advance them. I also wasn't going to start with the Gaea's pissed thing but since you mention it lets start there.
Top of chain is:
Big bad: This will require work because it's gonna be one of those Elder Evil tihngys Sign looks like Appauling Fecundity.
Bigbads Angels AKA The Dragon: Now I'd like these to be some inhuman plant critters, if there nothing natural we'll template something with the green bound template, or the Blightspawned template and let it roar.
Leaders: Likely Druids, and Warlocks of fey descent, I know thats likey 4th bleed but still.
Elites: Again Druids and warlocks of lower level, but also all variance of plant monsters, green bound and otherwise.
Brutes: We can easily find plant themed brutes.
Minons will be horde of various fey and they can be all over the place doing all kinds of things.
I think the elementals will be call into it, cause nature dudes tie to them easily so Unbeliever has a great idea there.
The primary enemy Race Will be Killoreen the second will be Briaxarus or whatver the spelling of that is statted to you're liking but we can also use combinations of thorns, nymphs, satyrs' and all the traditional nature critter as well as things like yellow musk creepers etc.
I'll go looking today for high level and or Templatable critters for our enjoyment...
So the campaign ends with the death of the bigbad and the ramifications of the elder evil sign reaching El 20.
@ Veekie again the purpose of this thread at least in part is to define that line as well. We don't want the players to run around not knowing what's going on, or CONSTANTLY be ambushed, but thats a part of the game sometimes thats going to happen, sometimes you show up to late.
However, at the end of this, its will be an Avengers adventure, not a JLA adventure, you will be allowed to inevitably punchout cthulhu with or without the maggufin.