I don't think the roaming Thundurus/Tornadus are that bad as Entei and Raikou in HeartGold/SoulSilver (or past versions). I enountered my Thundurus and used Strength on it, so it went to red health. It fled, but I just walked in the house and walked back our and it was raining outside. I encountered it immediately and used a quick ball on it. Caught it. It took no more than five minutes, lol.
Wouldn't suggest using a Masterball on Cobalion, Virizion, Terrakion, nor the genies. I haven't gotten Zekrom yet, but everyone says not to, so I probably won't. I'll save it for a shiny or maybe Kyurem if I just don't care anymore. Maybe I can offer it to someone for something valuable.