Is there a fundamental difference between a child of a military parent who is gone for a large portion of the time and Barret's actions throughout the Compilation?
Well there is a bit of a difference that the military is a job and Barret went on a soul searching mission. Although later, it turned out he did have a job finding oil fields, so it's possible that he does have a permanent job there, but rather than take Marlene out of a somewhat stable environment, he visits frequently.
But other than that, I was kind of thinking the same thing too. I was raised for a good part of my early childhood on a military base. Lots of the kids' parents frequently went on TDY, and if they were especially unlucky, both parents were in the army and they went away at the same time. Some kids handled it better than others.
I do have to agree with looney though, even with this, I just don't think AC/C did enough to really establish the core Barret/Marlene dynamic. In the OG, Barret's actions were called out, discussed, he thought about Marlene often- and thought about the reason he left to fight Shinra for anger, and eventually reached the conclusion that he would fight for Marlene rather than anger. It was an important point, but with AC/C it was just left unexplored.
But I think that's just the writers fault rather than Barret's.