The issue with mana points (esp. in EU4) is not that they exist, but how you get them.
Admin, diplo, mil, and money are all currencies in EU4, but the players have no problems with money, because you get it from logical, realistic, controllable sources - trade, taxation, conquest (indemnities), diplomatic gifts, etc. If a player invests his/her effort into having a better economy, they will gain more money.
However, mana doesn't work like that. Firstly, you get it just from the passage of time (3/month base + extra from rulers, etc.) which makes little sense - its not like it becomes easier to run an empire just because you've waited some months without making any decisions. Ruler stats aren't something you can control, making these 'currencies' seem more arbitrary and abstract than money.
Ideally, mana should come from related, controllable actions. So for example, mil points could be gained from investing in and maintaining a powerful army - staying at force limit, having maintainance maxed, drilling, fighting wars of conquest, answering calls to arms, etc.; diplo from maintaining alliances, having your dynasty on foreign thrones, etc.; admin from low unrest, running a budget surplus, being debt free, having lots of accepted cultures, etc.
TL;DR - mana is fine if it comes from things related to building powerful militaries, beaurocracies, etc. and not just time/having a good ruler.