So this is pure conjecture.
Hands of Havoc are probably going to have a "the only constant is change" vibe where they create things only to destroy them later. In some regards, they are the Revolutionary League (who were anarchists, but only insofar as wanting to tear down the old) and Xhaositets were basically another Kender/Malkavian/Chaotic Neutral problem on steroids. Giving the Rev league something to fight for (tear down the old, build something new) with the dadaism of Xaosmen (hmmm... no, let's start over again) gives both factions a bit more form and function.
The Mind's Eye is a better version of the Believers and Signers. The Sign of One was HARD to play (I know, I tried it) without being a complete jerk player, so rolling them into the Godsmen as they did (becoming a faction about following your destiny, self-improvement, eventual Godhood) makes them a lot easier to digest. My favorite post-FW change was this one.
I think the Free League will still exist, just as a minor faction. The problem again was that their belief was "free thinking" and "I do my own research" but they didn't have anything else in common beyond banding together to fight the oppression of the other 14 factions. It doesn't appear the 12 Ascendant Factions hold as much power or influence, so the Free League being the non-choice choice seems less important. I'm fine with the Indepts still existing in small pockets here and there.
Its clear this is again soft-reboot territory (with the factions restored and most of the factols returning) but considering how badly Faction War was received, I'm happy with the reboot. Faction War is about on par with the Prism Pentad and Requiem: The Grim Harvest in terms of changes that were hated by the fandom, so no complaints about ignoring them.