Personally I think it depends on the type of G4 collector you are.
For example - for G1 I am a completionist - I would like every pony and playset and every release together. However, for G1 even doing that it is usually easy to avoid doubles as seldom were ponies duplicated other than occasionally in sets where 1 pony finds itself released with both the first and second waves - Cotton Candy, Blossom, Starshine, Parasol, etc etc. But because of my need to have all sets complete, I have doubles of ponies like Starshine and Parasol so that they can be displayed with both the first and second wave of Rainbows as released.
However, for G4 I am a surface collector - only interested in one of each time of pony unless there is an obvious difference - so I have the wave 1 Pinkie and wont buy another single again. When I purchase the sets which contain her as I will display them loose, I either rehome or pop the duplicate pony in the trade bin.
I think if you are the former and like every set complete then you should store them and with time and perhaps when you have more space display each and every release complete. If however you are more a surface collector then perhaps you could release them from boxes and then sell/trade the doubles?
Such a tough decision!!!