I've only got Lucario and Absol out of the EX stages. It's really just a probability game on those ones.
I've finished with roughly 30 seconds left on the 2 minute ones multiple times and no luck, they still have a sub 20% capture rate (Maybe less?). Takes persistence I guess!
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BTW I think the great ball being multiplicative is a bit of a mistake - it needs to be additive for me to ever use it again.
If my capture rate is around 50%, thus a great ball providing a big rate improvement, I could just as easily try the stage again and have a pretty great chance of capturing. No great ball used.
If my capture rate is much lower (5% - 15%), like on most EX stages, because the great ball multiplies the chance by two, my rate isn't going to get much better and there's a pretty good chance I will have wasted the great ball. No great ball used again.
I guess it can be useful for people looking for an instant "second chance" without having to replay the level, (chance to capture notwithstanding) but if you're trying to use your gold effectively I think there are better options.