Unlike the first Mass Effect, the sequel will not allow players to restart the campaign with all the skills Shepard gained throughout his (um, her!) second adventure. Mass Effect 2 Lead Designer Preston Watamaniuk notes on the BioWare forums that the team is working hard to "offer a smooth progression into ME3 from ME2." The reasoning is that they "have to have reasonable knowledge" of where a character could end up at the end of the game.
Of course, Mass Effect 2 players can feel free to create a new character and start over. So, it appears that if you're looking to start Mass Effect 3 with a jacked-up Shepard, make sure to explore every little nook and cranny of the galaxy before going into the sequel's final mission.