I've identified my two biggest problems with the game. They ultimately don't ruin it, because there's so much else to love, but they're things that could've been vastly improved.
Field Skills - Every Blade has some kind of skill that can get put to use in the field, whether it's something simple as an element mastery or something more unique like lockpicking or superstrength. In theory, this is a neat system, because these abilities can be stacked or leveled to pass checks to progress or find goodies. In practice, they're aggravating, because only engaged Blades' field skills can be triggered. This results in a lot of menu management in order to progress in a sidequest or a main quest, when instead it ought to have just tracked all your Blades' abilities to save the headache. Grinds the pace to a near-halt at times, though it's typically more of a pain in sidequests than the main quest.
Merc Missions - There's one simple way to make these not aggravating: Don't require them in any quest. They should be nothing more than side things to run in the background for a bit of extra gold or EXP, as well as an easy way to level up your Blades a bit. But they often show up as a required part of a sidequest, so basically that step of the quest is "literally wait until this is done before you can progress." It's asinine and hurts the pace even more than Field Skills. When this happens, I usually go and do something else while waiting in the menu until the timer runs out; I thought I left pointless waiting behind with Majora's Mask. It's especially egregious because it requires literal hours of these to progress the quest of one of the best healer Blades just to get her highest tier of her skill tree.
Again, it's still a great game I highly enjoy and am still sinking hours into. These are just areas that need addressing to make for a better experience in the future.
Also there's a weird aggravating bug that racks up the in-game timer and I'm not sure what causes it. Something about suspending play during combat or a cutscene? But I swear last time it happened, I was in neither. Basically, I have an inaccurate in-game timer of almost 170 hours when it's closer to 110 according to the system itself. Kind of makes me upset, but small bug, I guess... Hope they patch it, though I harbor no delusions of such a patch fixing existing timers.