I m hosting some adaptive streaming video on windows azure and I have noticed that at the beginning the video start with the lowest avaiable bitrate. That is a big issue.
you can remove the extra streams (the low quality ones) at the server side either by hand (need to edit the xml files there, not just remove the physical stream files), or use IIS which provides facility to edit smooth streams (assuming you installed respective extension, say via Microsoft Platform installer app). Also you can use WinMerge or similar tool to compare a copy of the clip's folder you kept before using MS tool to see what it changes when you remove a specific (sub)stream from a smooth stream (compare the previous and the new version of the .ism* files)
that is also useful cause sometimes the player underestimates the client CPU and bandwidth (there are some custom versions available that are supposed to fix CPU heuristics issue, by having some config file pre-edited appropriately). That is if you have some screencast, sometimes client don't get stream of enough quality to read the text, so you have to remove lower quality (sub)streams and then it plays fine (you start removing the lower ones and see after which one it shows OK). You can also configure the TransformManager (or your code that calls into the respective functionality) to not create very low quality versions