Some suggestions because I don't feel I know enough about the game/wiki stuff to actually make these pages myself--at least not in any kind of efficient manner.
Links to elements on the card page seems redundant and not especially useful when you end up on the next page expecting something more like the elements pages and getting basically the same thing as the (uncategorized) omnilist at the bottom of the card page. If possible, make another section for cards listed by element (instead of alphabetically) with proper headers (instead of letters, obviously).
Overview pages instead of a list of links for creature, spell and permanent cards: like element pages. Leave the creature, spell and permanent links on the card page. --or the below ideas, which are a bigger undertaking (but more awesome).
Additional info tags to cards (hidden or perhaps replacing/adding onto "quick facts" on card page) that allow for a nice, sortable table to be made on the creatures/spells/permanents pages. Because of all the different tags that can be added to various types of cards, the tables would probably need to be broken down into multiple tables in some way.
Rough idea example: Permanents' sub pages Pendulums, Pillars, Shields, and Weapons each lead to a page with a sortable table. For example, the shields page would be able to sort things like element, name, damage reduction #, reflective yes/no, miss chance, stealable yes/no, destroyable yes/no, special yes/no.
Not sure how to handle upgraded cards--maybe different pages for upgraded creatures/spells/perms, linked on card page. Might not be too bad combined though.
Perhaps additional, specialized sortable table pages for cards that produce quanta (element, name, element of quanta produced, how many quanta, cost), poison, heal or whatever else might be useful. This might be too redundant if multiple tables are on the creature page for these things, but it would be nice to have all cards that do similar things in one place.
I think the sortable tables would be especially awesome to see an overview of everything you care about quickly. As a beginner, I know I would find it helpful for "finding that one card that does that thing that I need" and building decks. I'm not sure how much it would be useful to other players, but it seems like it'd be useful at least until they're able to remember all the cards and all their abilities.
Sorry about the long read, but I wanted to be descriptive.
Oh yeah: About the interactive deck incorporated with the deck image maker... what about bypassing the image maker and making it so the deck code produces a special thingie for the wiki? The (wiki-formatted?) codes would change into corresponding, linked cards--perhaps with a table for card count/cost/etc and with the un-changed code for copying. Might want a little tool to add a colon before each 3 character code or something for ease but I dunno if that's necessary with some kind of template. Seems easier than the fancy sliding, but I don't really know. D: