I think a lot depends on what you're using the bike for, as well as what you're comfortable with. For example, on a bike that you'll be using for a lot of urban riding, you probably don't want your feet attached to the pedals because you will be doing a lot of stop and go. For long rides without many stops, a lot of people swear by clipless...but then you have to have special shoes that aren't always so good to walk in and if you do have to stop suddenly for some reason, clipping out is one more thing you have to think about. (In case you can't tell, I'm one who prefers to ride with flat pedals and sneakers...just bought a bike off Craigslist that had toe cages and the first thing I did was get those off it after a somewhat nerve-racking test ride in downtown Portland.) You can always start with one thing and switch later.