As a hunter I've been playing around with the AEP (Agility Equivalence Points) addon in the past and am also a heavy user of Cheeky's Spreadsheet. AEP is no longer updated and doesn't include some vital stats (haste and ignore armor). I would assume that other classes also have access to tools similar to Cheeky's SS that allows you to calculate relative weights for all stats (for hunters it is about dps per point, but you could probably make the same calculation for healers etc). It would be nice if there was an addon that would allow me to:
1) set weights for all abilities
2) assign default gems for each gem slot color (so that it can be incorporated into the stats for the item)
3) calculate the sum of the stat*weight for the item
I don't expect the addon to do anything to come up with the weights... that is a far bigger problem. Rather this would be a tool to allow quick application of weights that have been previously calculated for immediate comparison between items.
If you wanted to be fancy you could allow the user to store multiple "profiles" with different weights. While this would allow the addon to ship with some default profiles, this might not be desirable since those would be more likely to be wrong than right.