I worked with a firm that used TD Waterhouse (now TD Ameritrade), and I'm somewhat familiar with Schwab. Their service bundles are all very similar. All will assign a back-office team to you that will help with asset transfers, account openings and so forth.
Each also has a portfolio management software package -- Schwab has what used to be called Centerpiece and TD has an Advent product + their online trading tool called Veo. I don't know that there are real advantages one way or the other -- just a matter of what you get used to.
In terms of selection, I think the biggest differentiator will be how a firm will handle you as a start-up. How much will you have in assets initially? Smaller custody shops will be more likely than Schwab to be accomodating if you have less than $10-20mil to start.
If I had to start an RIA right now, I would call an institutional sales person from each of 3 or 4 firms and tell me why they are the right one.