I think there's a good litmus test here for how they're going to treat the modding community. There was a screenshot I saw that showed the choosing, which had a logical progression pick, an unlockable 'if you have the right resources pick', and then an 'other civs' button which didn't show its options. Meaning, they did build a 'logical progression' into the system, and as a lot of people probably aren't going to like this feature that's probably the first thing people will try to mod is locking in that first pick only. Just because you don't have to pick someone else doesn't mean the AI won't.
One of the problems with Humankind's system I'd say is that while it seems incredibly flexible in practical terms it was less so. Each civ had a focus with a unique district to boost it: food, science, production, expansion, etc etc. so what you really wanted to do is string together a good balanced build and with AI taking options off the board that made things more limited.
Another thing I'm concerned/curious about is with the reduction down to 3 ages if they're simply taking a new approach or if they're slimming down and 'simplifying' things. In one of the videos there was a lot of comments from them how infrequently people actually finished their games to the end, which has a whole variety of reasons and would be really challenging to correct. While it's good they recognize it there's also a lot of wrong ways to address it, like in my opinion how in Civ VI they went from workers to builders.
One more thing, I think the introduction of commanders could be an unintentional big help. A massive problem in V/VI when they went to single unit hex grid, is that when you the player are managing tactics the best method is to form up in a line melee in front range in back and hit at the same time. But in both games they could never figure out the AI which just sent columns of troops at you letting you pick them off with much smaller numbers. This idea that one commander unit takes the units to battle and they 'spread out' on deployment could naturally give a much needed challenge boost.