@Sirdanest i'd have liked a small appearance even as a kind of shadow organization undermining the brotherhood or some Ex-enclave in the institute

Oh, yeah, they could have had "remnant" characters like the old ex-enclavers in New Vegas, but after fallout 2 it really felt like their days as a mighty army and super-power were probably over (as opposed to still incredibly strong, and were apparently only (at most) inconvenienced by having their base and president nuked in fallout 2.)
It sort of felt like the end of fallout 2 was almost for nothing, as they just popped up again with the same level of power and almost the same plan elsewhere. If the Enclave does make a come-back, I hope it's with a new story, a new purpose, rather than yet another power-armored army with yet an other genocidal virus or something. I'd like a new story, please.

@Sirdanest good point, maybe a takeover with a new president as a sort of post war government rather than a militant faction