Acquire data from Arduino at 1KHz

I want to make a real-time plot using data from ADC in Arduino (I need to do this at the frequency of 1000Hz). I wanted to know your opinions on how to approach this, I see a lot of posts online but none handles the problem of steady 1000Hz data acquisition. I have some ideas myself:

1) Using Arduino timer interrupt (more precision) and store the values in a buffer. Sending 100 values at a time (to lessen the Serial utilization).

2) If using an Arduino timer option (let the Arduino handle the Hz). I also need to send commands to the Arduino, for starting/stopping the data reading.

3) A send request method from Matlab and wait for a response (one value at a time) and let Matlab handle the 1000Hz frequency (my problem here is that it may not be that precise).

Some FACTS: As I can understand readVoltage (Arduino extension) is not that fast and could bottleneck the whole operation. When I use Arduino to stream data (continuously 100 samples at a time) I'm not able to send commands to the Arduino to start and stop. And all the real-time plotting stuff gets sluggish. Can you help me?! Thank you so much