I am not entirely sure if anyone has seen the article yet but a recent interview with Gamerzines, Mike Gamble says that it would not be a bad idea to keep your ME3 data. Read into it what you may, but to me it seems that the data could be used for a future Mass Effect title so it may be a good idea to keep your playthroughs.
http://www.gamerzines.com/xbox-360/news/mass-effect-3-saves.html