Really we do know what is canon. Right now it is the 6 movies before Disney and all of Disney's projects plus the Clone Wars Cartoon since it ties in with Rebels.
Everything else is in question to the point that it should not be considered unless referenced.
As far s Republic Commando series, the squad is canon, but the stories are not.
So basically all of the good stories is Star Wars aren't canon? As far as Omega squad goes, There has been no reference to them in any Disney projects that I know of. The only reason Delta squad is canon is because they showed up in the Clone Wars. Certain parts of the books could be considered canon such as at the start of Hard Contact. The only things I can remember from the books that conflict with Disney's Star Wars, Would be the stuff about mandalore. And the game could be canon aswell and was because it was the story about how and why the Republic came to Kashyk in Episode 3. If it wasn't for the reference to 36's squad in the first mission it would have no connection to the books that couldn't be easily explained.
I never got into the expended universe for Star Wars. So Disney ignoring it does not bother me. I think that is way I'm one of the people in the camp of really liking the new movies.
The last Jedi was good. Much better then the Force Awakens but in my opinion not even close to on par with the original EU. I think Disney should have just stuck to the EU. They already had thousands of stories that they could have made 100 movies out of.
Luke’s death ruined it