If you ride in muddy conditions, I would recommend the discs. A lot of bikes will come with U-brakes but have hubs set up to install discs. You'll save $ by getting a bike with U-brakes and if you end up hating them you can switch to discs for about $100-$150 more.
As far as pedals go...that's really a matter of preference. If you havent ridden in a while I would go with platform pedals. You can get yourself in a lot of trouble with clipless.