Well, the problems with seeming inconsistencies frequently arise because of the influence of Brannon Braga running the show. If you look at his track record as a writer and producer since he joined the Star Trek franchise, you will find that frequently things are forgotten because he does not feel they are important or he's going for something "different". This then has the effect of making it harder to explain how the timeline works.
More recently Enterprise was "brought more into line" with the TOS-type predecessor it should be by other elements in the franchise that overrode Braga. The design of Enterprise looks a lot like the Akira class because Braga ordered it that way because he thought it looked neat. It had nothing to do with any sort of logical progression of design lineage or anything else, they just thought it looked neat. But now that they're stuck with the ship and it's transporter it shouldn't have had, with its "phase-cannons", they have to make due. On the plus side those "drone-like" torpedoes they have are on the mark.
Interestingly, if you look at the early Trek work as being akin to Shakespeare as presented by the Ed Sullivan Show (i.e. the story works, but the visual effects were low budget at the time) then it works. If this were literature alone it would be easier to make it mesh. Since it's visual you have things like Klingons with no forehead makeup until the first movie because they couldn't afford it. In DS9's "back in time to Trouble with Tribbles" episode they made light of this "joke" and had fun, because ultimately it is not important.
As for the war, there are only two references. First, they're never supposed to meet the Romulans face-to-face.
Second, the war must be "fought with, what were by
our standards" (in terms of phasers and photon torpedoes) "primitive atomic weaponry" --i.e. early missiles, thermonuclear warheads, and torpedo weapons and "primitive" phased particle cannons, such as they are--"in ships that allowed no quarter, no prisoners"--feasible in large battles, where a ship like Enterprise or an early Romulan
Warbird class ship if it took a direct hit amidships would probably be destroyed, and without transporters.
Spock said it in ST VI: "You must have faith... that the universe will unfold as it should." Sometimes I think that was a shot by Nimoy at fanatical Trek fans that fail to see the forest for the trees.