Either/Or really. I'd say it depends on how many soldiers your managing. With a large number a class system would be quicker and less fiddly as you wont have to choose all the skill paths of each one, but if you its just a small elite team, heavy customization would work and could give players an extra sense of investment in their squad as they customize each member to their taste.
Or maybe both? you can customize each skill on a soldier, or you can assign them a class so you don't have to bother fiddling with that stuff and let it be handled automaticly if you choose?