I think the school of thought that starship design must be dictated by function first and foremost, and that there can be a straight line between each starship in each era is possibly not a useful assumption. (Trekyards on YouTube, which I generally enjoy, harps on this idea a lot.)
Here's an alternate scenario: I wonder if for example, while the two-nacelles-and-round-bussards might have been purely functional to begin with, perhaps the Constitution class mainly had had Phoenixesque nacelles as a design callback to the early days of Starfleet. What we thought was 2245 modern actually had strong retro influences. It might explain why the Bonaventure, allegedly the first vessel with warp drive installed in TAS (maybe better interpreted as the first ship
designed for warp drive installation), appears to resemble the Enterprise more than anything else. I think the novels place the
Daedalus-class as a design dating from the 2140s (that became more widely used during the Romulan War) so perhaps these two ships represent the Earth Starfleet of that period. The secondary hull of the Bonaventure becomes part of the
Daedalus design, sidelined until the Romulan War, while the saucer is used as the basis for ships like the
Franklin and
Enterprise.
The rounded nacelles continue to be used out of necessity, growing larger and more powerful by 2233, but requiring constant maintenance and monitoring. This necessitates the large ship and crew size we see in the
Kelvin.
Eventually warp engine design progresses to the point that powerful warp drives can be constructed without requiring massive rounded engines, freeing a new school of starship design to experiment with the angular nacelles of the
Walker-class. Maybe it's the breaking of the time barrier (whatever that is) that marks a brief return to the rounded Conchrane design for the Constitution class and other ships before some admiral gets sick of the nostalgia and arbitrarily decides that it's only square nacelles from here on out.

(The designers of the
Nova and
Sovereign classes might have been looking at the old
Walker design or ships like it for inspiration.

)
Regarding the Kzinti, while I think the four-wars-circa-2070/2100 is still compatible with Enterprise continuity, I can see where it might seem contradictory at first glance. But IIRC, all Sulu said was that the Kzinti fought four wars with
humankind, not that all of them were post-First Contact conflicts involving Earth.
We've seen plenty of examples of groups of humans at large in the galaxy prior to First Contact: descendants of those abducted by aliens (the Skagarans, Gary Seven's agency, the Briori, and the Preservers), descendants of time-displaced starship crews (
E2) and populations on 892-IV, Omega IV, and Miri's Planet which, while technically not humans from Earth, are culturally similar enough that they would probably identify
themselves as humankind.
Maybe the Kzinti conflict with humanity began with a lost Omegan colony or former Skagaran slave world. Who knows.
