I use .Net and Java stack, I don't want to start a war here but I never felt held back due to any reason for developing web apps in either of the two. For mobile apps, its a different story, I stick to phonegap.
I don't know that much about Java world, however what I can say about Windows + .NET is you are less productive. Why ?
1. Linux > Windows ( For .NET )
2. Python + Django/Flask are really powerful. Ruby & Rails as well.
3. You're basically writing and reading more code. Most of them is unnecessary. .NET is designed for enterprises.
4. Especially for startups, time & speed matters a lot.
I also think some of the above reasons applies for the Java world as well. Fantastic OS projects though in Java world.
I'm pretty sure you can make great web apps with .NET, but I don't get the impression that the ecosystem is very supportive.
I found a lot more support online for other stacks.
For example, I wanted to do a tiny webpage, and host it online cheap or for free. The cheapest options were Google App Engine and AWS.
I looked into Azure pricing and ran away. I'm probably ignorant of the best solutions (Rackspace seems to have a startup program, there was a .NET hosting I liked, there's also BizSpark), but most .NET hosting was a lot more expensive than I wanted, and not supportive of "weekend project" types.
