I feel like if Eureka: Anemos released with some of what Pagos eventually added (adaptations, bunnies, and warped-lockboxes) and some of what Pyros added (a few of the simpler Logos actions), and then built upon those systems with each new area, Eureka would have been far better received at its launch. Because Pyros, thus far, is easily the best of the three, having built upon and refined each of the systems from both Pagos and Anemos. NM spawn rates are comparable to Anemos, and leveling feels faster than Anemos, too. The adaptation and mutation system makes a return from Pagos, but the exp rewards for them, as well as the Logogram drops, make the system feel much more satisfying to take advantage of. The spider-web styled map of Pyros is much easier to navigate than Pagos, as well as being much more stealth-friendly than Anemos, although you still need to be careful of sound and true-sight based enemies in the higher level areas. And the bunny FATEs are back, but with more meaningful rewards for getting a treasure chest (ie. logograms), as well as a small amount of exp, tomes, and occasionally crystals for participating. No matter what I choose to participate in (NMs, bunnies, soloing, chaining) I feel like I'm making headway in multiple areas (leveling, Logos, or gear), which is just good design. And the various logos combinations add just enough variety to how--and what--I can fight that I'm excited to try out new combinations, even if some of them are just for fun (such as Watcher + Haymaker for evasion tanking, haha!). Heck, just as an example, I recently figured out how to create Bloodbath, so next time I go in I'm going to try fighting higher-level sprites on my Warrior with Bloodbath + Martialist, and see how well I can farm some logograms from them. And that's the sort of experimentation that you don't have in the rest of the game, which should have been the draw of Eureka from the beginning!

tl;dr, Pyros is really good. I'm not at 50 yet, and it seems like that will be the big time-sink, but at least the road from 35-50 is much more fun, and the Logos actions definitely help to spice things up in both solo play and party play.