First, definitely check all the connections and make sure the phase is correct for the center speaker (red/black)
Second, it is bad to stuff the center into a cabinet, so try to at least push it forward enough so the drivers are not recessed. But, it sounds like you tried that and it still is not clear.
A few things you could try.
1) If the center is above or below your seated ear level, tilt it so it is aimed at your ears.
2) If your receiver has the capability, simply increase the volume on the center channel by a few decibels and then see if that helps. I run mine at +3dB above what Audyssey recommended.
3) Try a phantom center. Unplug the center and tell the receiver you have no center. It will send the dialogue to the L/R towers. Maybe you will like it better with no center at all. You could try this with the 2000.6 speakers that you have right now as L/R or, as suggested above, the smaller 2000.2 ones you are using as rears.
Oh, Commsysman seems to always recommend setting the crossover to the sub at 60Hz, but most people recommend 80Hz. I don't want to get into that here.
Finally, unfortunately, many modern movies are mixed so that the sound effects have maximum impact at the expense of dialog. Often, the grumbly male voices are tough to make out. It may be the source material. I find that when watching TV shows or news, voices are easy to understand, but in many action movies, not so much. See if you can correlate when you are having trouble making out the words with what you are watching.
If none of that helps, and you decide you want a new center still, knowing the dimensions of the cabinet where it will sit will help people make recommendations. Try to post a pic of the entertaiment center. Pics always help also.