this is also an issue for final fantasy, how final fantasy 11 and 14 are online games yet for some stupid reason are given a number, same for dragon quest 10
here's what I think: if the games in a series are in direct continuation of the other, then a number system makes sense [jak and daxter, mgs, etc.], however if the stories are self contained or they just flat out have nothing to do w/ each other, I'd rather they ditch numbers and have a subtitle [zelda, fire emblem, etc.]