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I've seen filets served both ways. I personally feel that fish - especially trout - should be served skin down. I want to use a fork to pick the flesh away unimpeded.
But I've seen Jaime Oliver and one of my favorite restaurants in DC (Le Diplomat) serve trout skin side up.
Is there a best practice here?
I think it depends on which fish, and the way it's cooked. If it's steamed,poached, or en papillote, fish skin can be quite unappealing to some diners, and, as you say, the conventional way to eat the fish would be to lift the flesh from the skin, especially if at the same time you are parting the flesh from the bones.
But if it's an oilier or meatier fish, pan-fried or grilled, the skin can be deliberately crisped, in which case it's intended to be eaten. (This, again, is much easier to eat if the fish has been filleted from the bone before cooking.) In that case, it is sometimes more attractive, and keeps the skin crisper, to serve it skin-side up.
In a restaurant setting:
I think the best practice is that if the skin is nicely crispy and meant to be eaten, then it should be plated to show it.
If the skin is not meant to be eaten, then it should be removed before plating.
If the skin is unappealing, then it should be removed before plating
At home, do whatever you want to do.
