Season 3 is not bad but it suffers from structural problems. We already saw the Dominion War in DS9 and what was the Xindi conflict should have been the Romulan War, i.e. doing a season long arc about a lethal conflict makes little sense when you wanna do it all over again later. The Xindi are nice but also fairly one-dimensional, reasonable primates vs. hyperaggressive insectoids and reptilians (talking about primate speciesism).
Sure, on closer inspection the Vulcan three-parter makes little sense. It provided two reason for the aggressive behaviour of Vulcans and neither stands analysis. As you pointed out, it takes time for a text to actually influence a culture whereas the show pretended that it happened overnight. As the head of the Vulcan administration was a mole Romulan influence must have been and still continue to be massive so it can hardly vanish over night either.
But to be fair, few Trek stories stand analysis. Unification is a beautiful story yet the notion that it makes sense to invade Vulcan Trojan Horse style is ridiculous. You cannot conquer the Federation by taking one planet, it makes only sense as a large scale "take hostages, extort the UFP and leave" scheme. So if the Romulans have to leave in the end anyway they could take any planet, it does not have to be Vulcan.
On the other hand this assumes that Romulans behave rationally which might be true on an individual level but Vulcan and Romulan culture, the institutions that help them channel their strong feelings into imperialism respectively help them suppress their feelings via ridiculous rituals, are crazy. As taking back Vulcan is politically-wise the sublime object of passion for Romulans it makes sense that they do not calculate it as well as their other tricksy endeavours.
As you mentioned Fallen Hero I would like to add that characters are of course also important, after all the performances of Nimoy and Lenard influenced Vulcans more than any script writer. In this era ENT suffers as Blalock is not a great actor. She plays well but she is no Nimoy and among the other Vulcan characters I only found Soval convincing (take e.g. the torture scene with Shran in the Vulcan three-parter).