The obvious two to draw lessons from, are Cantr & FTO. What worked mechanically, and what doesn't.
Rot, is an important one, and in a few ways. A youngster, a peasant, a stoneage person, shouldn't have rot actually affect them much. A leader with vehicles, and buildings and in a hightech area, well, they have to make effort (or whip people to do it), to keep things in good order, and not slide down. At the least, that encourages people to work together. Or against, if that's what interests them.
Communication, and emotes. here, is one of the areas that FTO did slightly have over Cantr - an emote actually looks different to spoken word. A purely visual thing, and rather effective. But having a myriad of ways to talk (passing notes, using the radio, speaking to a group of friends instead of everyone at once, always), adds variety and possibilities.
There's a lot, but these are two areas that have a lot of promise. Of course, it's more important to get the resources, and good ways to get them installed first, before ways to lose them to the ether become a thing!
In addition to the idea of rot, which is probably needed for a Persistant world, or it will suffer from "Everyone's rich" inflation after a while... if you do decide to add specialized skills or magic or technological advancement, I wonder if there's any possibility of adding "randomness" to that function.
One thing, which I tried to do in my game, and was a bit odd "code-wise" was similar to Cantr's apothecary recipes. Once found, everyone can use them in Cantr. What if each character who attempts to use "Alchemy/Herbalism" it will generate a vaguely randomized list of "recipes" for that character. This would require a bit of Experimentation, but would cause challenges for "passing on the info" to apprentices, so has pro/con to the idea.
I've only played two character on FTOI who both died early (stupid hungry paretns?!?! and got lost, got attacked by beasts), but I do like the idea of emotes parsing with italics *he smiles* or slightly grey text, something subtle. Little thing like that goers a long way in visual Niceness, perhaps.
maebius' idea about random recipes is actually sort of neat. But, imagine past recipes. Depending on which skill level you are you would have access(or intuitive knowledge) to a certain amount of things encompassed in the skill. So, say you've got a good weaponry skill, you would get access to X amount of the total projects that could be made in metalworking, a lesser skill you'd get a lesser amount of projects available to you. This would encourage communities working together. I might have access in a skill tree to make an arrow, but might need another person who has knows how to build the bow itself to build it or show me how.
Then again that could be rather complicated and cause whinging from people who've got bunched panties over not being able to do everything.
It'd be nice too to see an inventory more representative of a character's strength for example. I don't know how you plan to handle that but in Cantr everyone ways 60kg and can carry 15kg regardless of strength. Realistically if you're weak, you should be able to carry less. Not to mention the whole weights of things in Cantr is nothing short of laughable. 300 g iron shield when a hawk is 1000g... seems a bit off to me. So my real suggestion I think is just appropriate weights and utilizing strength better.
Haven't been around much but I'm still looking forward to any updates. Meanwhile I really need to take another crack at Bubble...
Just a gentle prod to mention an off topic discussion board would be good for keeping chat going during down time on the actual game development. Though right now I'd probably mainly use it to ask what the heck is going on in Cantr. From the board it's been looking like players are leaving in droves.
My condolences Fizi, but really it's been a long time since I've been able to come up with a good reason for absolutely anyone to stay. Don't build sand castles in a bully's playground, etc. Same old story.