I got the best idea and I did that .
You remember the new critical capture system pokemaster talked about.
Before battling thundurus save .
Each time try a pokeball on the first shot and maybe the critical capture activates .
Other than that , You would need a pokemon with shadow tag , arena trap , etc. or move like mean look or wrap for a temp hold back for trying an ultra ball in red Hp also recommended sleeping move .
Well if you are not willing to waste the time on that just go for a masterball .