So back in New Super Mario 3D World, there was a lot of issues when it came to Emile. Was he just because he was the easy punching bag, or were they literally trying to envoke him as a Butt-Monkey and therefore the others give him a lot of flak unnecessarily-especially Masae?
I'm pretty sure the reason Emile got a lot more verbal abuse in that game was because they had Masae as their guest. Their previous guests - JoshJepson, Lucahjin, and Super Jeenius - were, while snarky, not really focusing their vitriol towards Emile unless he actually did something clearly deserving of it. Masae has known him for a while, and even outside of TRG, reacts to him more or less the same way Jon does, which is why it felt like he was being targeted a lot more for even minor things. I personally think it was overdone, but regardless, there's the explanation.
In the Brawl tournament, they had items turned on but in the Smash Wii U tournament, they didn't have items and fought on the Omega stages. Why play with different rules for the two tournaments?
Sort of Wild Mass Guessing here, but: They may have been experimenting with a more "professional" style, as most official tournaments (or at least ones run by "Stop Having Fun" Guys) insist on very strict rulesets with no items, stages without gimmicks, etc. I personally think it turned out less interesting than it could have, but it may have just been a test.
Also, to add on: in the opening rules, they say normal and omega stages are allowed. I think the players just kept voting for omega, it wasn't in the rules that they had to. The "no items" was definitely different, though.