Earthbound can be a real piece of shit, everybody knows the clunky and limited inventory is a pain in the ass, and it is completely true. Furthermore, the story, while good, lacks a lot of personality building for the main cast of characters, which is funny cause every npc has amazing dialouge. While the lack of character building doesn't harm the ending overall, it certainly does not hit as hard as Mother 1 or 3's endings, due to them actually taking a few moments to flesh out the main cast of heroes at several points.
Total War: Empire, a buggy mess that likes to crash in the late game. Unfinished, AI is illogical in both diplomacy and a lot of battle tactics (Which makes the few times they pull a clever maneuver incredibly surprising) and nearly requires modding to be playable, either through script edits or from installing overhauls.
EU4: Now this is one I haven't thought of much, but there certainly are many flaws to find in this one. First off, 93% of the gameplay is just finding buttons to press with the right timing, that's it. The DLC's have mostly been focused around adding more buttons to press. Powercreep has been a real issue, like how Spain will have colonized most of Oregon and Alaska before a Russia player can even hope to have gotten to East Siberia. Many intended paths require RNGesus to smile upon you, and whose alternative requirements can be very difficult to achieve in comparison. (So many MP games of my friends grumbling over many such cases.) And, despite being an 11 year old game, some regions are still not very fleshed out. India and parts of the Americas lack flavour and content. And of course, the UI can be a bit inscrutable at times, with a few features hidden away or poorly explained, like the macrobuilder diplo screen. And yeah yeah, the DLC policy is terrible as it locks out critical features behind a paywall, which has only been partially fixed with updates and working older DLC into the base game.