Granted, the look won't be quite as smooth as factory. I have a new Kenwood Excelon deck in mine. It's surround is black like the piece around it so it blends pretty well. You have a few options for the color displayed on the LCD. The closest match I could find was blue and orange so it's half way there. One item of particular interest are the new Alpine decks that are comming. You will be able to rotate the knob through some hundred thousand different colors so you could match it perfectly to the color of the dash.
Still, the quality of sound the stock system puts out is very very bad. Even just in comparison to other vehicles stock systems. It's probably the worst I've heard less say some vintage car's we've had that were that way for originality. I would like to have a stock looking deck if it were possible for it to have some advanced functionality and circuitry inside.
As far as stock decks with outputs, no. You could use an amplifier that accepts "line level inputs" where you'd hook the speaker output from the deck to the amp, but the problem with that is junk in from the stock deck means junk out.