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the only ledgendaries i caught in SS so far is Raikou, Entei, and Lugia. i use them, especially Lugia. only for like tough battles and stuff though. i cant wait too catch more ledgendaries! especially Suicune and Articuno :) oh! and Mewtwo :)
All my legendaries are in my box expect Lugia and Ho-Oh. I have only two legendary Pokémon on my team; Lugia and Ho-Oh. Strange but my Mewtwo disappeared from my box. Meaby my box was too weak for Mewtwo and Mewtwo escaped. ;)
My Lugia is on my SS team cause I love Lugia. Other then that all the legendaries I have are in a box dedicated to legendary pokemon, though I've been thinking of moving legendaries into boxes suited for their habitats.
I've caught all except for, if I'm not mistaken, Mewtwo, Articuno, and Rayquaza in HG. I'm not sure if I caught Moltres, yet, either. I can't catch Rayquaza, though, because I don't have a Groudon.
I boxed the ones I caught. The only legendary Pokémon from that game that I like using are Suicune, Raikou, and Zapdos. Zapdos I haven't caught yet and both Suicune and Raikou had unhelpful natures.
All I have to catch in my Soul Silver is Latios. Therefore, everyone is stored in my box and are probably not going to be getting the light of day any time soon unless I use them for the Pokeathlon or something. I'm not really one to use legendaries on my team; only time I have was Suicune on Crystal. :x