I have never really met any other groups, so I can't really speak on the matter.
Myself, I did use a few house rules. Namely, that you had to roll the lowest-tech table for your character's faction unless you took Well Equipped, and from there, you could roll on better tables. I didn't allow for "pick'n'choose" mechs.
The key thing is that I let the rules from Mechwarrior Companion (2e product), overrule anything from the 2nd edition core product, as the core product was filled with ridiculous amounts of holes, the first most obvious one being regarding grenades
- MW2e core says that when throwing grenades, you don't use the Throwing Weapons skill. However, nowhere in the book does it say the skill roll you're supposed to use. Luckily, MW2Comp fixes this by saying that grenades ARE decided by throwing weapons, albeit with a tn modifier representing that grenades tend to roll after landing.