Oswego, I am sorry the SQ is dissapointing so far. Have you not had a sound system in this room before?
Indeed the room acoustics is a huge part of what we hear. I have not heard the gear you have but I agree with adidino's point, essentially that it's unlikely that the speakers are harsh and have no bass (other than in the unlikely case of defective speakers).
It's likely the room. I have some of the same problems you do. My room is large, vaulted ceiling with hardwood floors and tons of windows. I had to do many informal treatments to calm my "lively" room with its high-end harshness and smearing echos especially evident when I turned the music volume up.
So I put up lots of lined curtains and a large padded area rug. I then strategically positioned speakers and MLP for a nice soundstage irt clarity, imaging and width. In my case the ceiling peak runs from right to left (so facing the front it's as though I'm looking at an amphitheater). So I moved the R/L speakers away from the front wall toward the center and did the same for my MLP, moving it away from the back wall toward the center. I was then in a 9' equilateral triangle with FR/L. This placed me more nearfield and thus reduced my hearing unwanted echoes from the ceiling and walls. By taking account of the curtains I in effect treated the side wall first reflection points, the front wall directly behind my speakers and some of the wall behind MLP. Those are the areas that are most in need of diffusion/absorbtion. That worked pretty well and I expect a similar strategy will for you too...for the highs.
To smooth the bass it takes similar but different strategies. In my room the bass tends to boomy, not thin but either way it is about positioning the speakers and MLP in the room so none are in severe room modes, the bass peak or null spots. It is also usually necessary and recommended to use bass traps to decrease the room's effect on the low freqs (under about 200 Hz). As mine is not a dedicated listening room, traps are not a good option. In my case pulling the MLP away from the back wall decreased the uneven boomy uneven bass somewhat.
But the problem is that optimal bass positioning cannot always be done in a way that satisfies the treble/soundstage optimization AND accomodates a multifunction room. So I used two accurate, musical subs carefully placed by measuring the acoustical response in the room to avoid exciting the worst peaks and nulls. I also rely on DSP room correction to further smooth the bass.
In your case try moving the speakers and MLP around a bit while playing bass-laden material to find a spot where the bass comes back. In general, getting speakers closer to walls (and especially corners) emphasizes bass. Your dealer should offer to come buy tto help trouble shoot and assist with positioning.