Is it possible to run Migration Assistant between two Macs with different versions of the OS X (Yosemite and El Capitan)? In my case, I'm looking to transfer some user accounts and apps from old Mac running Yosemite to a new one running El Capitan.
Yes. Quite possible.
The only difficulty would be if one of the users on each machine is 'the same person'.
It will not merge accounts, it will make new accounts for each migrated user.