What would be the best pokeball to use to catch Latios?
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I used my master ball on Latios/Latias. I suggest that you use a timer ball or ultra ball if you don't have your master ball though.
Nest ball if you don't have the master ball and remember keep your strongest Pokemon in the front.
Master Ball.
If you have already used this however, try to stop Latias/Latios from escaping with a pokemon's ability or move - can't think of specifics at the moment - and then weaken it's health really low, give it a status problem (pref. Sleep NOT poison, as it may make itself faint), and then throw heaps of ULTRA BALLS. You should catch it. If it faints or runs away, don't worry - it appears more than once (it did in R/S, and I presume it is the same for Emerald).
I, personally, keep the Master Ball for Latias/Latios, because it is harder to find and capture than the other legendaries (Rayquaza, Groudon and Kyogre being the easiest). Hope I helped, : ).
Or you can just level up one of your Pokemon to level 100 and throw apricorn made level balls
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