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Grouping by theme sounds like a good solution. Except possibly the CITY sets, I have a few of any one theme, CITY on the other hand I have a lot of. They can be in different places even which solves the 'shelf getting too full' problem!
I will be doing this in the new year and will try for a combination of baseball card sleeves for small, comic book for medium and leave large as is in a file cabinet.
Right now they are all in random piles in various boxes organized by when I got the sets (or autobiographically if you've seen 'High Fidelity'). It will be nice to get them organized by theme/year.