[Because the Bonaventure simply looks too NEW, that's why not.
Not really, going by the image we have the ship was tiny compared to the TOS Enterprise, using the windows the primary had only five decks, the wide part of the saucer was one deck, the secondary (again using windows) was six decks
Using GeekFilter's 200 meters it would have been tiny even compared to the later NX-01.
It just looks too much like the NCC-1701.
But we've seen similar designs going forward from the TOS Enterprise too, the Enterprise C uses the saucer-engineering- double nacelles as well. As do later designs.
This could represent a general optimum lay-out that in-universe designer tinkered with for centuries, but with few exception the designers never got too far away from.
Apart from some added bulk around the warp nacelles, the Bonnie could almost be mistaken FOR the NCC-1701.
Actually it look like a mis-shapen earlier design, which might that been the intent during TAS. The upper bulge on the saucer is asymmetrical, the area behind the deflector dish extends forward, the engine struts are unusually bulky compared to the TOS hero ship, the engines themselves are mis-shapen.
In order to literally be the first ship with warp drive, the Bonnie would have to look a lot more primitive.
The Phoenix did look primitive. The Bonnie, despite what was said, wasn't Humanities (or anyone's) first ship with warp drive.
What Scotty meant by "She was the first ship to have warp drive installed," is unclear.
why starship design stagnated
It didn't, it advanced through the years. Compare the Bonnie to the image of the future Enterprise (Enterprise F?) seen during ENT.