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Best advice I can give on that is to assume that your playerbase is stupid lol.

Iirc, there wasn't a prompt to build bakeries to go with the farms, I just built them out of common sense, but some could miss that they're necessary. Actually, come to think of it, I don't think I got a proper breakdown on farms themselves either, nor how fertility works. Like previously stated, I mostly relied on common sense and what I know from other similar games, but not everyone will make those connections right away. Another instance of this can be found in the woodcutter. The woodcutter works on rules that are not rare in modern citybuilders, but again, relying on your playerbase to already know some mechanics is not a great idea. Let them know that it will auto-replant trees after cutting, and avoid the guesswork. 

I saw a comment near the top talking about felling orders not being fulfilled - I'm almost positive that this is happening bc felling is assigned to jobless civilians, and the hauling of logs is assigned to labourers (I think anyway). I had the same issue myself and got around it by purposefully not assigning a few ppl to any job. Having free jobless villagers fixed it, and the fell order worked fine after that. If this is intended then that's totally chill, but again, having an "idle" or "jobless" counter in the jobs window, as well as a description on the things those villagers can do, would be helpful in clarifying that. 

Also the "find someone who can read these runes" quest is really open ended, it's not exactly clear how to go about progression there. And speaking of quests, the first mission asks you to build a storehouse, but there is no building by that name. Changing that quest (and maybe the preceding dialogue) to say stockpile would help with the ambiguity. There is also not a proper teaching moment saying that roads need to be built before other structures. I found out I needed roads first by looking at the "you can't build here" popup, which is a bit unintuitive. 

With the ruins exploration thing that you mentioned, I'm pretty sure this could be rectified by making the explorable ruins and the destructible ruins more graphically different. Especially the explorable ruins - there isn't much way to identify the edges of them outside of clicking on them, which some ppl won't do unless they want to try and remove it for building space. Making them more visually distinct would highlight them as structures of interest rather than free stone lying around. I never once questioned if the shielded temple was a destructible object, for example. Adding a bouncing arrow over the closest structure after reaching that quest might also help lol, at least that way ppl get a hand to hold when trying the mechanic for the first time.