Obviously I'm not talking about the obvious things like the certain look of each RPGM or the relative ease of using 1 or 3 in certain areas over 2. I'm asking in general is there any kind of system, scripting, skills, etc. that RPGM1 or RPGM3 can do that absolutely cannot be emulated on RPGM2? Any one come up with anything?

RPGM1 can have custom sprites.

Additionally, RM2 doesn't have the storyteller system.