I believe most all of these bikes use the Zongshen engines. Since manufacturers in China tend to buy a bunch of parts, slap them together, and put them through EPA testing, I think for consistency they purchase their engines from one source--Zongshen. That being said, some might use Lifan engines which would NOT be a bad thing, by any means. You are good to go with either engine OEM.
I personally like the look of the full-size XMoto bike over the Apollo, but as far as which one is 'better' could probably be compared to trying to decide between a new Ford Fusion or a Chevy Malibu...either one will be as good as the other off a new dealer's lot.
Choosing between any of the 125cc pit bikes is like choosing your favorite child. I would probably play eenie, meenie, miny moe to be honest...