One thing I liked about Font Reserve when it was still a good program was the flawlessness of the auto-activation in Illustrator and Quark. FontAgent seems to lag a bit in this department. For example, when opening an InDesign document, Font agent can't activate the fonts before InDesign reports to me that they are missing... but when the document finishes opening they are all active anyway.

Illustrator has a slightly different problem. FontAgent activates the fonts, but the blank space characters get substituted out with question marks (i.e. "Text?Headline"); if you close the document and immediately reopen it, the blank space characters render without problem. This is annoying if your file takes a while to open.

Fix these problems and you'll add some polish to what is already the best OSX font manager.