I wonder though: at least in early generations till tactics and expressed developed in real time space combat, if human instinct wouldn't default to thinking in two dimensional tactics?
It wouldn't, since three-dimensional combat tactics have already been developed for fighter planes and even submarines to a limited extent.
More importantly, people are going to be living and working in space long before they start FIGHTING there. The kinds of people who are likely to be involved in a real space battle are the kinds of people who have been in space long enough to stop making those kinds of mistakes; they're used to thinking in three dimensions because it's impossible to operate in space otherwise.
Give it a couple of generations of field experience rotating back into the training regimes and you'd have a Starfleet that would be capable of three dimensional combat as a natural form of tactics.
Considering the Klingons have been fighting wars in space for hundreds of years before Starfleet even develops phasers, it's unlikely they'd really have a "couple generations" to figure that out.