I have the option to choose either of those protocols to connect to my university WLAN. Which should I use? Does it matter? What are the drawbacks of each choice?
I would use TTLS unless I had a reason not to. It's tried technology and supported across more platforms.
Here is a good (if somewhat long) overview over at O'Reilly. Be sure to read the comments to the article for more opinions.
Here is a quote from the conclusion