Carrion Crawlers that carry undead plagues with rot monsters (ghoulish rust monsters that decay flesh) that spit green slime which can sicken....Kobolds behind siege engine traps like giant mechanical crossbows in reclaiming a fortress stronghold. Underwater adventures with things like Mermen and Eyes of the Deep in underwater submerged tunnels. Arcane artificer as an enhancement tree or even a caster class that can pump energy into energy cells that can be freely moved or placed in augment slots and charged accordingly (maybe instead allow them to be crafted in devices and then infused with arcane powers).

I like the synergy boss quests...a Giant Medusa that had a stone elemental beholder as her Guardian familiar set before her throne set in an arena with spectators all turned to stone would be pretty epic. Just brainstorming here while waiting for time to pass.