I always have the mascot Legendary on my team, no exceptions, given that the plot usually makes a big ol' fiasco about them, and it would seem like a shame to not train them. However, I usually box the other Legendaries simply because I'd rather choose Pokemon based on how long they've been on my team and how attached I've grown to them than by how powerful they are. This sometimes leads to me having teams consisting of wimpy com-mons I had since the first few Routes, so Legendaries tend to help out in a pinch.
However, I've a tradition of starting a post-game team; after beating the game, I box all of the Pokemon I had used up to that point and begin raising a new one. By that point, I give exactly zero craps about fairness, and as such my post-game team almost always consists entirely of Legendaries/Shinies/Pseudo-Legendaries/what have you.
All in all, I don't really consider using Legendaries to be a necessarily n00bish behavior, it's just played up as one waaay too often. Case in point, Sabbath, my Zekrom, isn't really all that stronger than the rest of my team.