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If anyone here has played Guild Wars, you'll recognize the idea immediately.
If storing the extra Rune Pages / adding Mastery Pages on the server would be too much to add.
There could be a possibility of having a form of template code that could be saved to the player's computer as a text file. With this, someone could have a rune / mastery template specifically for whichever champ they play, however they seek to play it.
Now, a fork in the road.
Instead of having just the 2 pages that a player can choose from, they would be able to choose from any of their saved templates.
Keep the rune pages limited to 2 options, with just the ability to load a saved template through the rune book prior to going into Champion Select.
Notes: This will likely end up being used on places such as LeagueCraft on Champion Guides. Obviously, it would be made so that someone wouldn't be able to download a template code to place into the necessary folder in order to use runes they don't have, as it would only load in what they actually have.