I organize my player cards in binders and boxes. Only one copy of each player card is in a binder (to keep the binder from bulking up) and the rest are stored in a box in the same order as they appear in the binder. I separate by sphere, then by Allies, Attachment, and Events. Order of cards after that is random, but newer cards I just place in their appropriate section next in line. I keep heroes in their own smaller binder (4 pocket sleeve sheets, stored in order of release).
I find this set up useful to look over the cards without the binder being so unwieldy (before I stuffed ALL player cards in the binders). When I need to find a card I know exactly where it is in the box and the binder (I get deck lists online and build them using my binder/box method).
I might try this. I've always had my cards in Dragon Shield Clear and a few months ago bindered them to facilitate deck building. However, I've noticed some cards are bending a little since it's a tight fit with the sleeves. This is the very definition of a 'first world problem,' but it still bothers me.