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The only disadvantage with skill caps that I have found is in opposed tests. The 1 hit cap for defaulting means that anyone using it in an opposed test against an opponent with the skill will almost always fail unless they use Edge, but I guess such is the advantage and relevance of proper training.
Indeed. But, if you've never held a gun before it's not easy to hit someone with combat experience and/or fast reflexes who is trying to avoid you. That's what wide bursts are for, though.

This is what really offends me about this optional rule, because anyone who wants to be good at something already has a high skill, and anyone who wants to be okay has a couple of points in it. The character that gets punished is the one who thinks he'll never have to use a skill (either because it's obscure-- like Pilot: Submarine-- or not part of that character's concept-- like the guy who doesn't use a gun), but then when something comes up in the game that would make it really cool if they did use that skill they know because of the skill cap there's absolutely no point in trying it. (And limiting it to one success does that, because the bulk of the system is either opposed tests or multiple thresholds. Any time someone is trying to stop you or you're doing something other than the easiest thing to imagine, it's going to require more than one success to have a shot.)
If I were playing in a game and something like that came up-- a vehicle chase was the example we were using earlier, but it could be anything-- and the group said, "We can't succeed, let's just let them go and do something else," I would be disappointed. To me, that's the antithesis of tabletop gaming.