For dedicated servers, spoilage rates and time progression have been the most difficult things to balance in my experience. Using conventional preservation methods such as pickling/curing ingredients, storing in cellars, sealing crockpots, etc work great for a lot of things, but there are some mechanics that are downright impossible if you play on a dedicated server where you only have limited hours per day but other players are running the time forward constantly. For example, cheesemaking: you've got to be able to be on during a window in which your animals can be milked (this is decently forgiving at least, but still difficult to manage depending on how frequently you are able to play). Then you've got to go through each of the steps in making the cheese, and the spoil times for each step here are not so forgiving, and there's not much you can do outside of modding to fix this. And unfortunately, the only "easy" fix to this would be a blanket reduction on spoil rates either globally or for certain containers (such as barrels), which could in-turn trivialize a major survival factor in the game. Perhaps more control of room temperatures and their effects on spoil rates could address this to some extent, but again, balancing making those mechanics impossible for casual players versus trivializing them for all-day players is a tall order. I'm curious to hear how other server managers are juggling this.
Time progression can also create difficulty in farming. I have not yet found an easy solution to this, but I am looking at greenhouses as the easiest fix: if you can make greenhouses work as a true safeguard for your crops, then you don't have to worry as much about your crops dying from seasonal temperature shifts before you get a chance to harvest them because you took a weekend away. If you could just throw your crops into a greenhouse and have the peace of mind knowing that they're going to be safe from seasonal shifts while you're away from the game, then that concern goes away. One suggestion I've seen mentioned in other threads makes a lot of sense, but I imagine would require quite a bit of rework to the code structure of greenhouses; the suggestion was essentially to make it so that greenhouses will never let a crop go below its minimum growing temperature or above its maximum, so while it would still be subjected to reduced yield and slowed growing rates if the temperatures are too extreme, they at least won't wither away. There could be an argument here that that also presents a major balance issue, though, in that players could then essentially use greenhouses as forever storage for crops.
Even with mods, I have not found a good existing solution to tackle either of these in a way that doesn't make the game's survival aspect too underwhelming for the players that are on far more often than others, and I'd venture to say that it may be the biggest sticking point that is holding dedicated server popularity back over anything else. The time progression works wonderfully for single player or for set playtime servers, but unfortunately it just unfairly limits the amount of game mechanics that casual players can participate in on dedicated servers, and that's a problem that needs addressing sooner rather than later since it is wrapped up in the core mechanical foundations of the game.