The MoBA comparison is makes a little more sense if it is directed at the PvP specifically. The problem is that it is only like 10% of the game. I am a bit puzzled why so many people even care about it since there are 728543 PvP games out there just like it, but the PvE is very unique and fun. Even assuming they don't allow any customization for PvP, you don't HAVE to spend real money, you can just PvE instead.
They initially made the classic mistake of most MMOs and tried to be all things to all people. That leads to inevitable failure. I think they realized what was compelling about their game is the PvE, so they said fuck it, and set up PvP to be MUCH easier to balance so that they don't have to spend lots of resources on it. In my experience it is basically impossible to make hardcore arena style players happy with balance anyway.
As for the new PvE, it is already has ridiculous customization. It has only been out like 2 days, the GUI is crap, and most of that time it has been unplayable so this is pretty easy to miss. In PvE, you are able to swap abilities in and out already. For example, I took the heavy turret off of my accord engineer and then put it on my Bastion frame. He is now a turret god and it is pretty fun.
Beyond that the customization in printing gear is amazing. You upgrade the restrictions on your frame and can then customize gear to fit within those restrictions, trading off stats on equipment as you see fit. The Mk.I upgrades are sort of all around upgrades, but you can go hog wild on the Mk.II versions. This relies heavily on planning and harvesting the right materials and then planning out what you will use to construct gear. It has more depth and thought to it than any game since Star Wars Galaxies. This exists right now in the new version of the game.
You can change classes anywhere on the fly by using a battleframe station calldown.