Synchronizing Timer: Consider that you are load-testing. Start 25 threads (with synchronizing timer disabled).
You will note that the start time of first thread will have a difference of about 800ms to 1000ms when compared to the last thread. This ideally is not a good testing condition for loads.
Now consider the same scenario with synchronizing timer enabled. You will notice that the start time of all the threads is absolutely the same. Ideal scenario for load testing.
Std Deviation: Standard deviation quantifies or indicates how much the response time varies around its mean or average. I would suggest not to judge the system performance based on Standard Deviation. In reality this just indicates how much the system is fluctuating. Nevertheless, Deviations should be minimum i.e. less than 5%.
GUI and CMD: Lets just say that on one hand, the GUI makes the program more intuitive; on the other hand, it consumes more resources. JMeter GUI should only be used for test development or debugging. Personally, I do not advise using JMeter in GUI mode if you are initiating an actual load test.