I'm in the same situation. I was using a Yamaha DTX500 but still not happy with the feel or the sound. I actually missed the feel of sitting behind an acoustic set more than anything if I had to choose.
So what I wound up doing was:
Bass drum: - Felt strips on both sides of the drum with a towel inside. I changed the beater to a Ludwig Lambs Wool. A Vater Vintage Bomber Beater would work as well. This considerably cut down on the volume. I still have to play a little on the lighter side, but it gives me a natural feel with real tone for the most part.
Toms - Vater Noise Guard pads (similar to the HQ SoundOffs).
Cymbals - I placed microfiber cleaning clothes over them, such as these:
http://www.amazon.com/Jobar-International-JB4048_Jobar-Microfiber-Wonder/dp/B000Y28KKQ I cut a hole in the center of each cloth so they can go over the cymbal post so they don't slide off. One per cymbal is fine, including over the top hi-hat cymbal. I still get the rigid feel of the cymbal, and a little bit of tone. More than using the rubber Soundoff pads. I'd say rebound is better than the rubber pads.
Snare - Sabian QuietTone pad on top of my snare. It's perfect for brushes as well (though you have to take some sandpaper to it) and it has a rim.
If I choose to use something like a Regal Tip Blastick or Vater Whip I can get away without the snare pad (though I still use a muffling ring) and I don't need the towels on the cymbals.
It does help that I'm home during the day when most of the people above, below and next to me in my building are gone, so I can get away with it. But even after 5 or 6 when everyone comes home I haven't had any complaints.