Both choices are good ones...
Probably the nicest thing about most decent AVR receivers today is they have separate pre-amp outputs for each channel. This allows you to use it as a pre/pro by just adding a separate amplifier. And some AVR receivers will allow you to assign where the on-board amplifiers receive their input signal allowing them to be assigned to the "B" zone. This can allow the on-board amp to power speakers in another room while the separate amplifier(s) power the primary listening zone, "A".
Also, most receivers are adding HDMI switching now.
Might want to also look for a good deal on the Denon 3806. It's received rave reviews from many other sources. Somebody else should hopefully chime in on the Yammie.
Is there an advantage to separates? Now days I'd say "NO". Most receivers have the same features (and more) for at least half the money of a good pre/pro. Granted, Emotiva has brough the prices down to where the average person can afford a basic "separates" system.
(For what it's worth, I have a B&K pre/pro and separate amps. Could have bought Denon's top of the line receiver for what I paid for the pre/pro
)