Most bioinformaticians I know are poor developers, have limited knowledge of existing algorithms, and/or have critically limited bio knowledge. As a result you get buggy, slow and unmaintainable software (see: all the MRI analysis software posts recently), reinvention of classical algorithms (anything from basic statistical tests to full on clustering methods) or tools lacking the full scope required to actually be useful.
I think MS could change this by having strong CS/SWEs with longer tenures than you see in academia, backed by more money and essentially unlimited computing resources, with a high profile name to win them collaborators who can share good datasets. (Compared with Google, they're not trying to generate data in-house as far as I've heard.) Some of the most notable advances in bioinformatics have come from applying decades-old algorithms that never made it to bio before then. Even if MS just accelerates this by applying people who know about these algorithms, that would be very helpful.