I love the web but I hate to work in the web. It is a shitty experience. Getting my data in and out can be a pain in the ass and slow. There is very little proper integration between services for obvious reasons. On the desktop I can pump data around in memory to other applications lightening fast and if I need to do something I can't do locally then I pump it into a cluster (cloud) service to crunch it.

Sure there are some desktop apps which suck as much as their web alternatives (Outlook for email is a great example) but overall I would much rather work with a dozen desktop apps than a dozen web services.

And then all of the other things you mentioned come into play such as code signing, no control over updates which might break my process, etc.