I would recommend trying to avoid strictly limiting the amount of times a skill can be used. The best example that I can thing of where this is seen is in Final Fantasy I on the nes, where magic spells of each level can only be cast a certain amount of times. It really doesn't work very well and ends up feeling way more limiting than a more simple resource system.
I personally feel that the best way to go about different skill costs is to use a sort of resource based system. Think of something like League of Legends, where characters may have skills that cost health, or mana, or TP, or some other regenerating resource. Heck you could even take it a step further, have a blood mage whos skills cost mana and health, or a warrior who hits so hard that he hurts himself. The possibilities are endless in how you can go about skill resources.
Otherwise you could look at the throw skill in Final Fantasy. Yes it's technically limited to how many times you can use it because of items you purchased, but it gives you the feel that you can use it as much as you want, even though in reality it's limited by a lot of factors (item count, amount of gold to spend on projectiles, etc.)
Overall my point is that different or multiple costs for skills can be very good, provided that it doesn't ever feel limiting to the player.