You don't normally get a choice, but if there are AB and B courses runing at the same time with slots available you will get to choose if there are no other restictions. eg. if you have a320 experience you may be placed on a short A330 course rather than an extended 777 course.
But back to the question: Do not pick your aircraft choice by destinations! They change regularly, and will surely change again when the A380 arrives and the a350 or whatever comes next. With rapid expansion comes rapid change, very little stays the same in EK for very long.
In the long term, no fleet is better than the other. They both are great aircraft, with good points and bad, and good destination and bad, also good instructors and unfortunately bad.
Most pilots are egocentric and want to think that they have the best of everything and so will talk themselves into believing their aircraft is better than their poor cousins flying that other horrible piece of junk. When you have a choice between modern wide body aircraft then there is not much difference once you learn how to operate it.