Both of these are great bikes. I'm not really sure how you are going to use them or your current level of skill. They are both fuel injected and liquid cooled. What are the features that appeal to you most? In line 4 cylinder is nice smooth power, parallel twin better on gas.
I think the two most deciding features of these bikes is what are they going to cost for insurance and how much weight are you going to be comfortable with? The GS650F is much heavier than EX650. If this is the two you are choosing?...The Suzuki will be better for long term ownership...
I would recommend a few more...Yamaha FZ6 (fast, powerful, good brakes)(the half fared one) the new full fared is a turd. Also a SV650 (torquey twin). There are many other bikes that would come into mind but these two would rate highest for me.