I chose to have an en-suite, because you're going to be living with complete strangers. You know nothing about their cleaning habits or hygiene in general.
I'm really glad I did. As my flatmates seemed to have any idea about living standards. I do not want to ever know what their bathrooms were like, especially when one of them said they hadn't cleaned their toilet yet, it was the 5th week of Uni for crying out loud!
Having that separate bathroom was a god send. However much I tried to keep that kitchen clean, it would always be a mess. Having the en-suite meant at least I had my own area clean and tidy.
Now yes next year (four weeks tomorrow) I'm living in a student house, but I will be sharing with people I've become really good friends with. They too care about keeping the place clean, plus I feel like I would be able to tell them if they weren't pulling their weight.