Yes. The yeast variety will give the beer some pretty distinct charactersistics. I am not familiar with the "San diego super yeast" but each variety will work best a certain temperatures, create various levels of esters which we detect as flavor, and different yeast strains will tend to reach different levels of attenuation. Attenation will affect how much residual sugars the yeast will leave behind when the become dormant. Also, some yeast will leave the beer with better or worse clarity. Wyeast is very predictable and good quality. If you plan to brew frequently, find a yeast that works for several of your favorite recipes and start culturing your own yeast to save on money. I mostly use the Wyeast American ale II for my IPA and APA brewing. I also use it in certian porters.
Lastly, whichever yeast you use, make sure it is healthy. Yeast that has been dormant for a long time will have suffered a lot of attrition and the yeast that does survive will be slow to energize. Learning to make a yeast starter and using yeast that you know is active and healthy is a good piece of mind.