The new formats are on the horizon, sure, but that horizon is still very far away. Even if HD-DVD is released in early 2006 as Toshiba has promised, players will be very expensive and content will be scarce. Then you will have to have other compatable equipment like a TV with HDMI to be able to view them.
A good universal remote is a MUST HAVE, IMO. You will use it everyday. Given your two choices, I would choose the universal remote.