I love the Box System (thanks, Bill and Lanette!) Very efficient, and allows you to organize Pokemon while offering several options for Box naming, Box background wallpaper, and even mass Pokemon-moving at times. Generation 3 definitely helped a lot of players IMO with the institution of the "auto-redirect feature", where the Box System automatically sends a Pokemon to the next available empty space in the
System if the capacity of the "current" Box is full. "Any-time access" would probably be even
more convenient, but I'm fine with the system as it is now. And as Kenshin5 mentioned, even if you release a Pokemon, the Pokedex still retains its info and marks/labels that Pokemon species in question as "caught" in the Pokedex listing.
My thoughts are what alternative is there or what do you have in mind that would be better then the current storage system? Do you propose a Pokemon Ranch or have them housed at your Professor Lab(as in the show)? Basically I have no issue with it and don't even think about it as opposed to other pokemon related things.
Strictly housing Pokemon at the regional Lab would be quite tedious IMO...rather than having the number of Box System access points equal to the number of a region's Pokemon Centers (number of access points is increased if other locations have PCs that are enabled to connect to Bill's PC, like such a PC in Hoenn's Weather Institute), a regional-Professor's-Lab-based system would reduce the access points to just
one, and you'd practically be required to Fly back to your hometown's Lab any time you wanted to withdraw a Pokemon, or spend a lot of time just making the journey back home just to withdraw/deposit one Pokemon. :<
I'm not very clear on how
My Pokemon Ranch holds Pokemon, but it seems intriguing...