I'm sitting on a lot of Mastery Tokens

...that I can't upgrade because I need to use all my blue essence on champions. Is mastery supposed to reflect my proficiency with a champion, or my ability to afford the upgrade?

It seems like blue essence is an unnecessary tack-on to upgrading your mastery. Just make it require more tokens. Mastery shouldn't be tied to your ability to afford an upgrade if its purpose is to show proficiency.