My first play of this version was with an old custom faction and old custom hero. In this game all the medium and above quests were locked and while they said they still required heroes, ereogs journals, etc researching them didn't allow you to accept them still.

My second game was with default Altar and all quests were acceptable at any time without any tech.

My 3rd game was with a newly made, but identical, custom sovereign and an old version custom faction (civics and master scouts) and had the same problem as the first.

There's also no way to delete the old factions and I have quite a few which, I assume, are all unplayable.

I'm running the first beta release with every patch installed as they came out so maybe the patching process needs a look too.