It was 10 years old and full of prototype technology. By the time of the signing of the Federation Treaty there were newer and better starships in service.
I was going to ask what prototype tech. But I suppose you can say the whole ship, since this was the first Earth Starship. But, at the same time it was the same technology that became standard for starships in the future. When I think about prototypes, I think about concept cars. They are far out there ideas that are being tested but don't actually make it to the final design for whatever reason (i.e. cost, space). So when everything on that ship becomes standard, it doesn't qualify as a prototype to me.
The ship got old, I mean it's like asking why we don't drive the Ford model T
Starfleet was beginning to field warp 7 capable starships, meaning that the NX class was now significantly slower than other ships of the line.