In case anyone is into number crunching as much as i am, i made a spreadsheet to help you compare gear
http://www.reddit.com/r/FFRecordKeeper/comments/33ovpg/equipment_optimizer_v01/
The idea is that you can list all the items in your inventory along with their current upgrade level and a realm synergy you want to know about, and it will compute the final stats of each item, applying synergy bonuses where appropriate.
You can think of it as optimizing the process of equipping something, going into a dungeon, checking the stats with synergy bonus, then checking the stats of a different non synergy item and seeing which is better.
It does more than that though since it can compute stats at an arbitrary upgrade level so you can see how an item you just pulled might fare after it's been upgraded a few times, which might help you decide if it's worth keeping