I'm not a fan of the back 3, especially with the players in the three that Everton have. I don't think Ashley Williams is up to it, he was serviceable against Chelsea, but offered nothing when Everton have the ball. Similarly Jagielka looks a ghost of his former self. Keane looks promising but he also looks a little inconsistent. He'd play better if he had someone more experienced (and decent) alongside him.
The problem with the back 3 is that it leaves one short in midfield so ball retention is harder. Against a team like Chelsea, you just don't play one less in midfield. If your forward moves into the midfield, then their defenders can push higher up the pitch. Again, its also a problem, especially if you don't have pace to exploit behind the opponents defence (Siggy, Rooney don't and Sandro didn't get any balls over the top). The wings are also vulnerable as its a huge effort for the wing backs to track all the way back. That's where the first goal came from, from Fabregas taking advantage of that space between the wingback and the left central defender.
At the same time I see Koeman's dilemma right now, he can't play two central defenders because they'll get carved up with the amount of pace all the top sides have, Chelsea, Man City, Man U, Spurs, Liverpool, Arsenal.
The solution really is to get another top tier central defender so then Jags AND Williams can sit on the pine. It will be a miracle if anyone sells a top defender this late in the window and I doubt Koeman is getting one this late, so its probably why he's been persistent with a back 3 even though it didn't work in preseason.