If I judged based on replay value, my GBA games would be far superior than most of my console games. It's about far more than just replay.
Most people hate comparing games with even the slightest differences. For that matter one should never say 'x' game is better 'y' game because they're different, but I find that stupid because at times it's obvious when one game is better than another, even across genres. No matter how different they are, it will be fairly obvious that Zelda OoT is better than some mediocre game like M&Ms Racing. It's because even though we may not be able to express it verbally, people draw lines when comparing games, and if it can be done with games with obvious disparities, it can be done with games with not so obvious disparities (like comparing OoT and MM). I personally judge the depth of a game when comparing it to another, and by 'depth' I mean how many different avenues of entertainment are in a game, the extent of the effort put into those avenues, and the extent of the effectiveness of those avenues as they relate to the game. This, at its core, still boils down to subjective tastes, but I feel that in general these taste issues will be generally more agreeable from person to person(just like how people can generally agree on good literature.) It's a much better ****ion, to me, than just saying "Games are too different to compare."
As far as OoT vs OoT3D goes, *insert 3D=more depth joke here*
