The new system is set up to choose the top 4 teams, regardless of conference affiliation.
again, probably not when you look at what has been said: LINK
The championship game will be managed by the conferences and will not be branded as a bowl game. The presidents also announced the creation of a selection committee that will rank the teams to play in the playoff, "giving all the teams an equal opportunity to participate." The committee will consider win-loss record, strength of schedule, head-to-head results and whether a team is a conference champion.
When you look at those listed criteria that makes it a long shot for an at large who didn't win their conference to make the field.
1) Win/loss records are unlikely to help at large teams that don't win their conference; their W/L records are similar generally (MSU, UCF, Baylor, and Alabama have the same records this year).
2) Strength of schedule won't help teams like Alabama or LSU unless they have scheduled more aggressively out of conference. Note that Alabama this year had one win against a team in teh top 20 of the BCS (in LSU) whereas conference champs like Baylor, MSU, and Stanford may have better quality wins on their schedules (again, I refer you to the BCS rankings of teams like OU, tOSU, Oregon, ASU, and UCLA compared to Bama's best team beaten in LSU)
3) Head to head results - another way of saying win your conference. If you lost those games against teams you should have beaten to win your conference you are going to have an uphill battle to an at large berth.
4) Winning your conference - By definition this will not favor at large bids.