I think the only way your going to get both speed and resolution is to make it dual range. I would use a second charge pin with a different charge value. Each setting would have to be calibrated individually. You could make it auto ranging by having it test for low capacitance first. If it takes too long have it discharge and start over at the higher setting. I would also have it test for 0V before starting the first test.
Keep in mind that you only have so much precision to work with when measuring time and voltage. Optimize for one end of the spectrum and the other suffers.