Because they are outclassed by the things in higher tiers.
Especially other legendaries. These Pokémon either have too many weaknesses, weak (stats wise), a bad movepool and pointless abilites. There may be some others but this is all that comes to mind for me.
Take Cobalion and Virizion for example. Justified? Nothing is going to be hitting these things with Dark type moves. I know there are Pokémon with the same typing (and ability in Lucario's case) in higher tiers, but they have better movepools and abilities to help them out.
Cresselia may have nice bulk all round (however a bad defensive typing) but those measly attacking stats will be doing no damage and its ability doesn't help it. And Meloetta with Relic Song is a very risky play.
The fact is that these things would be destroyed in Ubers, where most of the other legends are. Tiers are also based on usage. Clearly these things aren't being used enough as if they were they would be in higher tiers.
Hope I helped with your confusion :)