Most of the top offensive threats can 2HKO or even OHKO Wynaut (I'm thinking Gligar, Gastly, Taillow, Aron, even Shadow Ball/Dark Pulse Croagunk). That doesn't mean Wynaut is bad by any means, it's just that it's usually going to get one kill per match if it's played correctly (which is true for basically all of LC OU).What makes Wynaut unbroken in LC as compared to standard?
It is possible, though not exactly easy. I wrote a detailed guide for LC ev training which can be found here.
Besides pokemon being level 5, and the use of berries, what are some big difference between LC and standard battles?
I see 244+116+116=476. I think you may have added incorrectly.