-the fact that PoE gods are more like sentient manifestations of ideals/concepts rather than just petty, fickle beings with incredible power ala D&D/the greek pantheon. Because seriously, that much pointless drama only belongs in reality TV. If you're going to add drama, employ those on characters people actually care about.
-the fact that magic boils down to soul energy, and that soul energy explains why even non-magic classes can do what they do (non-magic classes regularly performing superhuman feats in other games is a personal pet peeve).
-the choose your own adventure-type interactions - there's plenty of room for improvement there too like narration, a bit of animation (even if it's only the interface), etc. These are great mini-games that also tell a story.
-the fact that each culture in pillars seems to have its own unique idiosyncrasies, like how female godlike are not seen as women in the Valian Republics or how Twin Elms is in some ways actually more civilized than Defiance Bay or the weird thing they do with powerful landowners in the Aedyr Empire (see Aloth's dialog)
-little things like people standing around smoking pipes and stuff. We need more of these IMO.
-the fact that whether the gods are "real or not" is supposed to be such a big deal. Is there a universally approved definition of "god" in Eora that we don't know about? So what if the PoE gods are not the equivalent of creator deities? These beings already care about issues that fall within their sphere of influence, they do have incalculable power, and they even try not to influence the lives of mortals directly. I mean that already puts them in the top 10 of "gods who aren't assh*les" list.
-not enough NPC banter. I expect more from NPCs, even if it's only exposition (like Sagani telling you about possible logistical dangers while you're adventuring around in the White March, for example).
-the item histories could benefit from better stories (convert a wacky everyday experiences into item descriptions if you have to), and there is hardly any flavor text for spells/abilities and the like. An occasional something like Fan of Flames: "Rumor has it that the wizard who created this spell, Ortagonus, was secretly a draconophile." or Chill Fog: "In the Valian Republics, Chill Fog is widely used on a mixture of churned cream, milk, sugar and eggs to create a popular frozen confection." was an unfortunate missed opportunity IMO.