Same reason why we treat 2/4 and 4/4 differently.
Your decision to give certain beats more or less emphasis is a subjective one. You can glean absolutely no information about a piece from the way the rhythm is subdivided, except maybe the intended tempo.
So, for example, lots of pop/rock music gets notated rather arbitrarily in practice because it's mostly about the feel from recordings anyway. It's common in that world to see what classical convention would call incorrect notation. And since the core notes all work still and you can go by the feel from the sound you know, it doesn't really matter.
But the classical conventions include ideas that the subjective accents you describe are in fact implied by certain time-signatures.
Similar deal with 3/4 v. 6/8. In 3/4, you have 3 beats per measure, subdivided into halves (duplets). In 6/8, you have 2 beats per measure, subdivided into thirds (triplets).