I agree that a new method of ordering the cards needs to be made, and the sooner the better. The more cards there are, the more initial confusion.
My thought was always to separate it into permanents, creatures, spells so that pillars/pendulums would be right at the top, or maybe even in their own category. Pendulums still aren't really introduced too well, so when they are in the middlish with 'P', I don't think that that will give them quite enough attention.
Also, rares aren't always on the edges, I have my trident and arctic squid imbetween purify and ice dragon, while even my nymph is on the wrong side of my water pendulums. Always confuses me when I see a little 7 or 8 and I urge to repeatedly click it and watch the little electrum count grow.
It's probably a good time to add this to the common feature requests, since I'm seeing this as pretty important. I'm biased, and I like it.
Good suggestion Rastafla