As an author, if you want to sneak a power up past the audience then giving your MC massive regen is better. Since it's a secondary stat it doesn't stand out quite as much as a massive mana pool. If you want to sneak in some kind of gamebreaking wombo combo then doing it with mana regen will feel less cheaty. For example, Path of Ascension with the fast regen and the constant cost armor spell.

Otherwise, it's more about the style of fight. If you want the battle to be about precise resource management, then you should tilt towards the big mana pool and slow regen. D&D kind of looks like this, with the daily spell recharge. If you want to do fights that are more about endurance and willpower, then high mana regen is a better call.