From a smallish amount of experience with Ubiquiti's gear, the Wi-Fi parts are far better than the Unifi Security Gateway. And you can certainly use them just fine without a USG.
I can only assume they'll be moving away from MongoDB soon, given the licensing situation. And the new Cloud Controller Gen 2 is considerably more reliable, which it achieves by the highly dubious hack of containing an internal UPS so that it is less likely to shut down uncleanly and thus die a horrible death.
The IPv6 situation is, indeed, embarrassing. But that, too, is solved by just not using a USG.
edit: None of this is particularly unique to Ubiquiti, IMO. By committing to using the same system or vendor for routing and for wi-fi, you make upgrades harder and you get stuck with feature sets you may not want. Home networks where the wi-fi is the cable modem or the wi-fi is the NAT/router box have the same problem, and it's even worse if you start using the same object for NAT/routing, wi-fi, smart home stuff, and NAS. Yuck. I wouldn't want to run an enterprise network where I've committed to using the same gear for routing and wi-fi.
It's a bit of shame that it's so hard to do a good job with wi-fi gear from multiple vendors, but getting things like fast roaming to work right is a huge pain without someone's proprietary management stack involved.