Scaling will be a difficult (but welcome) problem though SQL Server does not have to cost quite as much as most people think it does.
Microsoft could, however, offer more incentives and assistance to startups who choose to use their platform. They've made a lot of progress in the last few years toward being more developer-friendly but they need to go even further.
Finding talented ASP.NET / C# developers willing to work on startups can also also a challenge.