I don't think you have done anything wrong? You bought a great pair of bookshelves, a solid receiver, and seem to be on the right track. The next step is to just listen and enjoy! Kj made some good points about room interaction, you definitely want to mitigate hard surfaces if possible, but not everyone can have a treated, dedicated space, so don't go crazy worrying about it.
How are your speakers placed in the room, stands? Getting your placement correct is one of the most important aspects of this hobby. Good speakers placed poorly will sound bad. Your receiver has YPAO room correction and a mic, have you run the setup and let it adjust settings for you? This will attempt to smooth your frequency response of your speakers and sub. Some people don't like the EQ'ed sound, others do, so try it and see!
What kind of source material do you have other than the TT? Good speakers can reveal poorly recorded music, and it does not sound good. Listening to CDs or lossless audio rips is the way to go.
Denon AVR-1713 | EMP E55Ti | EMP E56Ci | EMP E5Bi | BIC F-12