lets see, nested items down layers that don't help you find what you need based on various stats, or a way of searching for items by most of the common effects? It takes 2 button presses to find any item in the new store. Took 3 or so in the old, and that's if you knew where you were going. Also new store has this feature like everyone is forgetting.... Its called a search bar. You can type in a word, kinda like google, and find the item your looking for.
On top of that, the recommended items are much better and help people learn to build for how the game is going, thus helping the player base become better players.
Also also, you can still customize your recommended lists for champs, with just a little searching of these here forums.
I would say simplifying the finding of items over some crazy (and stupid) nested system that people only liked cause its how it's always been, is about as smart as saying women belong in the kitchen cause that's how its always been. Sometimes you have to step back and get over yourself to realize that a new way is a better way. Games die when a vocal minority thinks they know better than the silent majority.
Riot made a much simpler, much easier, much much more intuitive shop. That is Keeping It Simple..... Stupid.