Given the trade-offs, I'd go for the larger over the smaller frame, taking advantages provided by the endurance/comfort (compact) frame design. For example, a 56 VR (Felt) has essentially the same reach as a 54 SuperSix but not the downside of a higher standover (but then, maybe it's a bit heavier but a little extra alloy isn't that much weight)...
A compact geometry means that you get a lower standover for the same (virtual) frame size. This seems like a nice feature in a mountain bike. It probably makes the bike a bit heavier than a standard frame since (I'd guess) that seat posts are heavier than seat tubes and the top tube is longer than on a standard frame.
Depending on what you want in a bike any of these choices can result in a good fit. So some of it comes down to what looks good to you. (ibid.)