In the main rendering (the one posted earlier, looking at the tower from above Dewey Square), there appears to be one semi-uniform streetwall on the eastern side of Atlantic Ave. The building directly next to the South Station terminal also appears to be in the same style, a sort of continuation of the existing building.
I really like both of these ideas. (Didn't the South Station building used to extend farther down both Summer and Atlantic Aves?)
In the uncropped version of the Atlantic Ave. elevation, found of page D4 of today's Globe, there seems to be absolutely no attempt to give the development any sort of cohesion or regularity at the street level. To my eye, it looks like a cluttered mess.
(By the way, in the cropped rendering posted here, the existing bus terminal is everything from the center to the right side of the picture.) The rest (from that brownish-looking element, on to the left) is currently just space open to the tracks.
So, my suggestion would be this: continue with some sort of uniform height and texture all the way from the station building to the terminal building. There should be several distinct buildings, with several entrances reflecting the different uses of the new buildings, but I think they should all conform to a more traditional look (some real stone would be nice, and with a project of this size and expense, I'm sure they could afford it). Save the modernity for the tower components, all of which appear to be set back from the street anyway.
Here's a link to the bird's eye view of Atlantic Ave:
http://local.live.com/default.aspx?v=2&cp=r1rqgs92bxyp&style=o&lvl=1&scene=2980227