Strictly from a marketing point, while it may be superficial, the store interface cycles four games in the main banner. At the moment, none of these are Valve games. Even when EP2 launches there will still be three open slots plus the four quarter size banners to advertise alternate games (Although I can see this logic failing because of the Portal/TF2 bundle).
Then there is the top sellers and top rated tabs. Six of the the eight games are Valve games in the top sellers. Which sounds reasonable considering Valve games rolled out on Steam for the better part of Steam's incarnation and, of course, because it's Valve's network (This is a ratio I don't see changing much even though it may be somewhat unequal). Next is the Top rated games according to metascore. The eight slots are split 50/50 between Valve and other publishers. So, the fair trick to having a stronger presence in this particular area is to create great games (which get great metascores) that are distro'ed on Steam.
Apart from the conflict of interest issues, the store interface is well weighted as of now. Obviously there is room for improvement to market other publishers but, I guess, this is one of the conflicts; will Valve allow that to happen?
Miller's concerns are all valid but, I think, most of his public flames towards Steam are because he is bitter because of Triton's failure.