The worst is kyogre in emerald because it uses rest when its health is low. or even worse it uses double edge!!!
Groudon of emerald is bad as well.
He is immune to thunderwave. all sleep powder and spore users become toast from a fireblast that too in the sun. And if u barely paralyze him (using stunspore and sacrificing ur grass poke), he too uses rest.!!!
haven't catched much but
when you use so many turns throwing ultra balls that the legandary struggles itself to death... that seemed to happen to me every time i went to catch the regi's in ruby and sapphire
All of them if you don't have a Master Ball, ESPECIALY roaming legendaries, they are ANNOYING to catch!