Mets team collector here. I decided that I wasn't going to get involved with the gimmicks of modern cards, such as colored parallels. And although front/back combos weren't an issue for me, I decided to simply go the route of every Topps base card from 1962 through present day would be my focus.
I finished it a couple of years ago and now just update it yearly.
As far as storage, I use
http://www.ebay.com/itm/330484751308...%3AMEBIDX%3AIT
The boxes are great and come in different wood finishes, so I use different boxes for different collections.