The option to sort by rarity, spell, permanent and so on, does not really make sense for me.
How do you make decks ?
Mono / Duos / Trios: You choose 1 or 2 colors and take cards from them. Colors are the best way to sort cards.
Rainbows: You have to balance the usage of quanta. The option to sort them by spell, perm, rarity makes a bit sense.
Nova: Similar to Rainbow
So I think colors are the best way to sort cards.
The only thing which could be sorted better are the cards within an element, but I think they are mostly sorted by the date, they were added. Older cards first. Except pendulums and nymphs (and I think I found some exceptions like "Reflective Shield before Morning Star")
I also support, that "Show All" should show all cards.