I'm not sure if any of these ideas have been mentioned already (forgive me if they have), but here are a few that I think could help users who sets up and edits thousands of pairs manually.
Custom Groups: Where the user can create groups and assign pairs to individual groups that share a global kerning value.
Character Search: Where a simple glyph search can be performed and the results listed in a column, with a search option for left, right or both.
More Kerning Window Options: Like a re-sizable window and maybe showing multiple kerning pair columns.
I've been using FontCreator Pro pretty heavily, I like the ease of use but I wish it had some kind of basic ligature support.
Thanks for a nice product guys.

