Building MIDI-Controller with 60 Faders [noob]

I've set my ADC's to 16 cpu cycles per clock cycle for a drum trigger system and it seemed to work well. For every ADC read, it takes about 250 cpu cycles (tested experimentally).

You got 60 analog switches and a response of 20ms (50 checks per second) should be good enough. To get constant values from your ADC switches I think you'd need to take at least 5 readings and make an average. Multiplying all that you get:

250 * 60 * 50 * 5 = 3.75 Million cycles, which is well below the 16Mhz capacity of the Arduino, so you should be ok.
For the velocity sensitive pads, you should definitely go for piezos. I've done a short program for that, but it's quite cpu-hungry at 1Mhz per channel. It's pretty precise, but I'm sure you could do something easier if you search on the net.