Mine sounds great, but then I am not you. The key words in your question, at least from the lack of specifics given, is Or was this more of a statement and not a question?
I have the DVD-2200 hooked to a Yamaha HTIB. I am using the 5.1 analog for DVD-A and SACD and a Digital Optical cable for movies. The model number for the Yamaha HTIB is the YHT-100. It includes 5 small speakers and a 100 watt subwoofer. I am not using the subwoofer the came with it, I am using the Yamaha YST-SW305 200 watt subwoofer that has dual 8" drivers.
It is probably more a result of your speakers. Those speakers do not have the ability to truly playback all that DVD-A and SACD can offer.
My guess is that the Yamaha HTIB uses a higher crossover (like 100hz or 120hz), where the 2200 has a 80hz crossover. Therefore you probably have a sizable hole in the midrange.
You might try running your main speakers through your sub and using the crossover on the sub set around 100hz. Then tell the receiver and DVD player that you do not have a sub and have large front speakers. It will direct all the bass (including the LFE channel) to the fronts which will still go the sub, so you will not be missing anything. That may help tailor the crossover to your speakers which could help.