1) Hard to give the PCs fate points - They use them quickly and it's hard to give them some kind of inconvenience every scene so they can get them back.
Well, as others have said, they don't get Fate points every scene. Also, Fate is not earned through inconveniences. It's earned when you allow your characters Aspect to generate interesting complications and unexpected plot twists. So, it they want Fate they need to start thinking of cool ways to interact with the story. That's not solely the GM's job.
2) Having to use fate points to gain bonuses - So one of my characters wants to take cover in a fire fight but he has no fate points to tag the aspect 'crates.' As I understand it, you can't use an aspect unless you have fate points. Seems very counter intuitive.
You can hide behind the crates, but if you want to add +2 to your roll you generally have to do something, i.e. a maneuver to generate a free Tag or spend a Fate point to invoke the aspect. I'm not sure why it bothers some folks that they can't get everything for free in life, but it does. Sure the crates are there, but it's all abstracted. Are they effective cover? How about if he moves a few feet (still within the same zone mind you)? Are the creates effective now? Who knows? It's all make believe in our heads. Spend a Fate point and you get to say that the crates are making you harder to hit.
3) Complicated magic system - anytime the wizard wanted to do something, it took a while. And I have to admit, I often got fuzzy on how if you succeed on a evocation, do you add in the power to the success of the casting? I just felt like it could have been made simpler.
Evocations aren't really that tough once you get used to them. For attacks, roll Discipline and add Power, just like a weapon adds its weapon rating.
I'm really not trying to start a flame or anything, I just want to try and save this system for my group. they want to ditch it and go with something like primetime adventures or wordplaly. I feel kinda bad thinking I dropped almost $100 bucks for a game I'm gonna play 3 times. Ugh.
PtA is tons of fun, but that's really a very different game. Hopefully, they'll start enjoying it once the Compels are working properly and Fate is flowing.