I think the game could be improved if the bonus items you can get from clearing two/three star missions (not shop items, excepting the one absurdly priced sword) had some special effects to them; they're rare, you get a decent amount of them, you can't get rid of them... and the majority of them are strictly inferior to what you'll have in a few missions, if not outright inferior to the items you can buy from the shop by the time you actually clear the mission (I can't recall exactly, but there are some missions on extreme that require either some levels or very careful placement to perfect, and if you level up by advancing the story, you'll get better store items by then).
It doesn't have to be a huge thing, but just some minor bonuses; the master of archers armor could give a bit of extra damage to archers, the sheep master's staff could cause the priest to deal 100x damage to the god-sheep (considering it's a healer, I don't think that would be overpowered), the swords could cause additional bleed/poison/grant armor/give life-leech, etc. Just some minor bonuses to make it so that using unique weapons is not a totally inferior strategy.
If implementing bonus effects to weapons/armor, or making them give stats besides just damage for weapons and defense for armor, is infeasible, they could at least give bonus "ranks" in certain skills, e.g. Honor's Vindication could, when given to a knight, make them act as if they had a couple extra ranks in counter, or something.