1) Learning rate
Learning rate does not affect game balance in any way.
Even if it did, the solution is to completely remove learning rate from any stat in the first place because that has always been a terrible and self-contradicting idea.
For instance, in Fallout 3 & New Vegas, basically every single character must take 9 Int and then not gain a single level until they perform a specific series of exploits to get the +1 Int surgical augment. This is because Int determines how many skill points you gain per level and therefore your character is weaker the less Int you have regardless of your other stats. This of course adds absolutely no enjoyment to the game and only punishes the player for choosing a free character build and free play style - you know, the things these games are supposed to encourage.
It's a complete lie for "intellect" to determine learning rate to begin with. That's determined solely by how dedicated you are to the skill you want to learn. There are plenty of very talented and distinctly quite stupid home cooks, warriors, artists, etc. both in reality and fiction. "Intellect" is not a linear absolute that makes you "smarter" at every talent under the sun.
Please remove learning rate from any and all stats, and absolutely do not add yet another stat solely for learning rate. That would be a superfluous vanity stat, as everyone will just max it out anyway, so you should just remove it and treat everybody as having maxed out Wisdom.
2) Running out of MP
This will not be an issue in Fractured.
In most MMOs, characters don't run out of MP unless they're fighting for a really long time, in which case they will bring MP regenerating thingies. This will be more expensive if you have less MP but at any high level of play you should be able to afford it anyway.
The main reasons to fight for a really long time are raid bosses and grinding. So far as I am aware, neither of these is an element of Fractured.
Even if it was, the trade-off for mages is that they are very squishy and run out of health faster. If they heal with MP, then they are now running out of MP instead of health.
The mage's higher MP pool will also be balanced by the (presumed) idea that mages will consume MP more rapidly than other classes.