I wouldn't say nes and master system are the same as xbox vs ps2 and the cube
master system has quite allot of sought after games wich are very pricy including trash filler title grails. let alone the same kinda genre's unlike xbox wich has a focus on different genre's you got your zelda clones, your rpg's your platformers shootemups. and just allot of good games in general.
Also even though master system grapics are overall better with exceptions, it's soundcard was kinda mediocre. so it's not a win for master system by default, if where talking the multiplatform games on multiple systems, let alone that in them olden days the same game could be totally different per console. This isn't xbox ps2 era with pretty much the exact same product for a multi platform game after all.
The only thing that keeps nes games more pricy is especially cardboard for cib collectors. plastic cases are just far more durable. you could pretty much compare it with snes vs genesis. Master system for the good titles is not a cheap hobby I'd say. cardboard doesn't last and the difference between cib and lose cart is huge. if it wasn't for cardboard nes would be a hell lot cheaper for cib products.
That the nes is more popular absolutely, but the master system didnt sell that well so prices are pretty high and the supply especially for the good stuff isn't all that great
Still superior Xbox versions being undervalued depends,
Since majority of those superior xbox multi platform games are not the kinda games that people might replay on any of the 3 consoles today so those should probably never rise that much in value if the games aren't played that much in the first place, and the few that actually matter do increase in price if where talking xbox. examples like marvel vs capcom 2 and fatal frame exist after all.