At the moment I'm in late-game (continent 4, could kill the overlord any time) so my boring bits are kind of specific.
1) I've been gathering tons of enchant containers and I have yet to see a single "legendary" enchant, whatever they actually are. Since I'm something of a completionist, I'm going to want to get all the achievements, so I can see this getting tedious to the point of insanity.
2) Swamp dungeon level 10. The bug in the current version (1.013) is the only reason I managed to get this. I've delved down at least two dozen cave systems in swamp areas over continents 3 and 4, and I never found one with more than 9 levels (2 of them had exactly 9 levels and they were both on continent 4). If, as I suspect, it's impossible to get a 10-level dungeon until continent 5, you might want to say this somewhere in-game. If not, raising the odds of the dungeon going deep enough might be nice.
3) Buildings. I don't know what the odds are of seeing a shape matter guardian scroll, but as I previously mentioned I am on continent 4, I've grabbed every single building scroll I've seen on this continent, and I have a total of 13 buildings in my settlement. Maybe adding an expensive purchase to the white guardian stone which gives you a random shape matter scroll? The possibility of getting useless extra copies seems like an effective deterrent to abuse, meanwhile I can collect upgrade stones during the hour I wait for new missions to spawn (as it's virtually inevitable that none of them will have shape matter rewards). Of course if I've overlooked an important means of getting these scrolls, having a note which points it out would also be nice.
4) Plums. You read that right, plums. My current continent has exactly 3 squares of abandoned town, and 0 grassland with groves. I've gathered all the plums I can from the towns, so in order to get more I have to use "gather resources" to generate a mission on a town square and hope it's an outdoor mission and further hope that it has plum trees. But now I'm just nit-picking.
I'd also like to agree that the initial search for secret rescue mission rooms when you get to a new continent (until you get an apothekineticist, a lumbermancer and a stonebinder, along with the buildings to be able to cast "seek survivor") is tedious. On my continent 3, I found at least a dozen secret mission rooms before I found a rescue mission, and eventually I got an apothekineticist after I had 3 lumbermancers. A note on where best to find secret rescue missions might help, and it also might be nice if you tweaked the missions to always give you someone with a skill you're missing, if possible, the way that "seek survivor" scrolls seem to work.