I, like you, used Aperture for a while and got tired of how it discards all the correction information in the camera. It also does a rather crappy job working with RAW files, I think they look terrible. What Aperture's strength is that is does an amazing job at Content Management, so to me it's just a Library with my stuff.
I edit my photo's in Capture NX2 with Nic Color Efex 3 Plugin (no longer produced). I can do 99% of anything I want with this setup. It's not Photoshop, and I cannot get crazy, but I can get so much out of post processing the files than with Aperture (or Lightroom, but that's just my opinion). I then save both the JPEG and the RAW stacked in Aperture, with JPEG as the master.