If there were pitched battles, be it WWII or LOTR style, then it might be reasonable to see SOLDIER operating in large numbers. If they were an army of ninjas and assassins, ie a guerlla army, then it would make more sense to deploy SOLDIERs in ones and twos. Thought you don't like the idea of guerilla warfare, MOG, that does seem to be what they are fighting in the DMWs, and history shows that when a force is outnumbered and outgunned, guerilla warfare is their best option. It isn't firearms but remote control warfare that has begun to do away with the big set piece battles of old, but it's true that Gaia has moved on from Napoleonic style warfare, especially with its mecha (are they remote controlled or do they have some kind of primitive AI?). Which makes it likelier that the Wutai war was very much a guerilla war. IMHO.
No doubt at least some of it was a guerilla war. However, whether it was or wasnt doesn't really have much to do how SOLDIER is deployed. Don't forget that SOLDIER isn't the backbone of the Army, the actual...Army is. SOLDIER can afford to be deployed in small numbers (I think one or two is too small, maybe less than ten) because of their strength and skill, similar to real world special forces like the Navy SEALS.
If there were pitched battles, that wouldn't make a difference to SOLDIER being deployed in large or small numbers. I just think that they could have at least have 5-6 man squads displayed in the game.
I never really got the impression that Wutai was that much outnumbered and outgunned. If Square Enix used the Japanese-American dynamic during WWII as any inspiration for the Wutai War (and it seems like they did), it would be quite the opposite, with waves and waves of Wutai soldiers holding every piece of land and small island to the death with surrender not being an option, which frankly, would demoralize and scare the shit out of the Shinra Army soldiers, much like it did the Americans.
However, the downside to this type of warfare, is if you lose, you fucking
lost, big time, economically, militarily, and in every other way, just like what happened to Japan (and Wutai as well). Yes, Shinra did win in the end, but even with Shinra's *gasp* ROBOTS, it didn't really seem mismatched. I can easily imagine Wutai fighting the shit out of Shinra with large scale battles all over their main island, the smaller surrounding ones, and the Western Continent and the seas around it.
The whole 'ninja/assassin' thing used to explain away their entire combat presence to me, sounds corny, and while yeah, of course they had these, I figure it would be more of a special forces thing, like their version of SOLDIER or the Turks.