I think you guys are making this more complicated than it needs to be. We're talking about two separate publications here:
Game Player's was a multiplatform magazine from Signal Research that ran from 1988 to 1991. It has a clear beginning and end.
Game Player's Nintendo Guide was a Nintendo-only magazine. After it was acquired by Future, the magazine became multiplatform as of issue 6-6, dropping Nintendo Guide from its title.
Ultra Game Players is the same magazine, same numbering scheme, same focus, but with a title change.
Game Buyer immediately follows Ultra Game Players, but has its own numbering scheme.
If it's important to separate these magazines, I suggest the following:
Game Player's (the original Signal Research magazine, stands on its own)
Game Player's Nintendo Guide (covering 1-1 through 6-5) becomes:
Game Players (starting with 6-5), becomes:
Ultra Game Players
Game Buyer is then its own separate publication.
Whichever way this database handles the change from EGM2 to Expert Gamer/Electronic Games to Computer Entertainment/Electronic Fun to Computer Fun/VG&CE to Video Games should be the same way it handles Game Player's Nintendo Guide to Game Players and Game Players to Ultra Game Players - same publication and numbering scheme, but a title change.
Whichever way we handle Electronic Games (90s) to Fusion to Intelligent Gamer should be the way we handle Ultra Game Players to Game Buyer - continuity of publishing schedule/staff, but new numbering scheme.