Substitute is a huge problem for me, the way I get rid of it, is using a mass amount of attacks from all my Pokemon until they eventually get themselves so low they can't sub, I'd also suggest having a recover user on your team, it allows them to get rid of substitute, and even if they don't work... Gengar would be the next best score, especailly using disable...
sorry, this doesn't help, and I'd just suggest teaching some of your guys Calm Mind, and Recover, allowing them to receive bulky boosts, and even occasionally destroy sub users.
I hope this was a little helpful, and I know PB people will tell me I'm wrong, that you need this and that, but the more bulk you have in your team will allow safer wall breaking.
