I design User Interfaces for a living for a software development company, and if I might make a few suggestions for design concepts that make the shop more quickly navigable:
1. Get rid of the drill-down to access the different sub-menus of the shop. If there are 5 categories under magic, then just put five small buttons on the home screen and group them with an outline or something. Clicking into a drill-down menu system means extra clicks and adds additional time the user must spend reading category names. Your core userbase is young people with good eyesight and dexterity with a mouse, so take advantage of it.
2. You need to be able to switch and save the default ordering of the items in the category lists. When I look through the item list in a category, I'm looking for an item that gives me the best bonus in the particular stat that I clicked on, reguardless of how much money it costs so I can build to it. Other users may care about the order by price, but it doesn't do anything for me personaly. For % vs #, make a grouping divider that visually separates them and label the groups plainly.
3. Don't show items that you can't buy ever throughout the course of that game. If an item is specifically for twisted treeline or dominion, don't show it at all on summoners rift. Showing options that will never become available confuses a user and makes them wonder why they aren't available, and in this case, that confusion means many seconds off of the field. Also, this increases the size of the page and makes scrolling to 2/3 the way down to get to the best items rather than just all the way (adding to the precision required to use the categories)
4. Make use of some kind of visual cue for which items have auras or other unique abilities that a user might want to be drawn to. You can use a colored border or some kind of in-image icon or something more creative, doesn't matter, but it would be nice to see.
I am also a fan of the favorites idea, and the auto-buy queue, those would be really cool, but they are of course more complicated to implement, and they may add exess complexity to the shop if not implemented in a seemless user friendly way.
I like the idea of filters as well as sometimes I'm looking for an item that adds AP and HP at the same time, and filtering by those two categories quickly would be really helpful.
Also, I'm not sure if this is a factor in your decisions, but perhaps making it take a couple of seconds to navigate the shop to buy something is intentional as part of the gameplay experience... I'm not sure about that, but I'm sure that you strive to keep the shop navigation speed about even between new users and experienced users.