Hm. One of my #1 pet peeves with game design is the addition of difficulty through not providing information. In Solium Infernum for example, you can't see the benefits of a manuscript piece that you are examining in your deck or tribute screens. This is problematic, as I am left unsure what to do with them - does this apply to a legion, praetor, enemy, or buff my avatar? Only way to know is to check the Bazaar or the wiki. Information in strategy games should be readily available.
My second issue is anything that relies upon grinding. I do not like repeating myself in a very static way, especially if the reward for doing so is not guaranteed. I prefer unique challenges that give unique perks. That saves me a lot of man hours, so that I can spend them on enjoying the actual game.
The third issue has to do with the unlocking of perks: If they are reliant of a certain difficulty level to be selected before a savefile is started, then that is a problem - requiring psychic powers to do the right thing ahead of time is bull. When designing the game difficulty selector, make it state in no uncertain terms of what, if anything, requires a difficulty level.