It depends on whether you want to emphasize the strategic or the tactical aspects of the game.
Note that while it is natural for DMs to assume that strategic thinking is "better" than tactical thinking, it may not be what some players are looking for in a gaming experience. Such players (Robin Laws has called them steam venters or butt kickers) might just want to blow off steam in a game, and having to manage resources across encounters may make it seem like too much "work" to be enjoyable.
As a DM, I don't like per day abilities when they make the fights too easy for the PCs (sudden maximized fireball kills all opponents in the first round of combat), but I like them when they are used to turn the tide in a tough fight (PCs are taking a beating, then one of them pulls out an ability that saves the day). One way I thought of to balance that was to have offensive abilities to refresh per encounter, but defensive and restorative abilities to refresh per day. That way, I will be able to calibrate the encounters to the PCs' (relatively constant) offensive capabilities, while relying on their defensive and restorative abilities to kick in when the dice turn against them (hopefully not more than once per day).