Why is it then, in Smash Bros. Larry's trophy description states that he is the leader?
Because it's inaccurate. Just because the trophies say so doesn't mean they're correct, trophies in Smash Bros can be wrong a bout a lot of things (like Shadow's trophy in Brawl, says his first appearance ever was Sonic Heroes, even though he really debuted in Sonic Adventure 2). Wendy's trophy states that she sees Peach and Daisy as her rivals for whatever reason. Peach might be slightly understandable, but how in the hell can Daisy be her rival? They have never interacted with each other ever, and the only game they ever appeared together in is Mario Kart 8.
Anyhoo, Larry isn't the Koopalings leader, his trophy description is inaccurate. Ludwig is the one with that honor, and was Bowser's 2nd in command before Junior replaced him. In support of this, Larry is said to be the youngest of the Koopalings in terms of age and in the Mario game's he's usually the first one of them to be fought, and isn't quite as powerful in battle as some of his peers.
Just read this right over here:
http://www.mariowiki.com/Ludwig_von_Koopa
Sorry for the late reply.