Added sorting ability in links palette would be very useful.
Allowing me to sort by file size, alpha, date placed, date altered. Similar to finder or windows explorer. Allowing me to rearrange the columns to suit my needs.

A preflight indicator of any potential conflicts would be a nice add as well.
CMYK doc with an RGB image placed. Unused nodes swatches, does this doc contain any overprint items, that kind of thing. In a perfect world I could set in prefs what I want warnings for.