As for .NET, the fact that most startups don't choose it should probably send a pretty strong signal to Microsoft that there is something wrong with it. On the other hand, the .NET team could simply be happy targeting "enterprise webapps" (non-startups), in which case there is nothing wrong with .NET, and something wrong with their acquisition criteria.
So basically, if Microsoft really wanted to pour that $44 billion into buying every up-and-comer, they need to pay attention to the team, and not the implementation, and then back that up by not forcing everything it buys to be rewritten in some Microsoft-sanctioned technology.
That is why the Yahoo acquisition has never made sense to me. Either Microsoft is going to spend inordinate amounts of time converting Yahoo's LAMP stack to it's own ecosystem (and fall way behind Google/ebay), or they are going to finally run a LAMP stack themselves, which seems to undermine the .NET ecosystem (not eating their own dogfood, etc).
Of course, they could fix this problem if they gave up trying to create a parallel, all-Microsoft stack and made their stuff play nice with everything else out there on the wild wild web (with less effort wasted on duplicating existing open technologies).
But that would require Microsoft to make the transition to providing a service (support/training/_ahem_ ad placement/etc) rather than a product (windows/office). When the product simply becomes a means to get people to pay for your service, suddenly giving the product away and making it play well with others is a great idea.
When Google was spinning out new apps every week a few years ago, everyone accused them of just running a lot of loss leaders to feed traffic to adwords. Well of course that is what they were doing. The fallacy was thinking that the apps were supposed to be individually profitable. In reality they are all just 'products' that get people to pay for the 'service' (ad placement). Of course they are going to provide all these products for free. You don't charge people for business cards do you?
Microsoft is trying to do this I think with their subscription model stuff. The problem is that they just charge too much, so there is still an incentive to get around paying. It's like high taxes provide an incentive to find a loophole, whereas low taxes are just easier to pay than avoid. If they gave away Windows and just charged some low amount for automatic updates and remote assistance, they'd probably have a workable business model there. Whether it'd be as profitable as their current model is another consideration.
Anyway, I'm significantly off topic, so I'll rein it in. Wasn't expecting my train of thought on this to run on so long. In summary, I think Microsoft is hosed unless they open up their ecosystem and play nice, and unless they find a new way to give away products and charge for services.