I've released an update for Wineskin... version 2.6.1.
I think I've fixed all the El Capitan bugs and it should work fine on 10.6 - 10.11 now.
* important point. This has to change how an engine is installed in a wrapper slightly. If you update a wrapper to 2.6.1 and it does not work right, please reinstall the engine in the wrapper. You can just use Change Engine and install the same one back in, but it will install it correctly for 2.6.1 and then things should work right. Newly made wrappers should have no issues.
Please test 2.6.1 and let me know of any issues. I'll try to fix any new issues that may be found for a 2.6.2 soon if its needed.
You'll be able to get 2.6.1 in Wineskin Winery as an updated wrapper.
Sorry for the long delay, and not having these issues fixed before El Capitan was released.
If you get stuck with a wrapper that just goes "Cannot be opened" then Right click in the wrapper and select Open the first time you run it.