The biggest thing is the lack of integration. Some of them have patchy SSO integration options, but most won't tamper with the app in any meaningful way, so even if you have login integration, you have to log into each app on a server, and each app is subject to that app's capabilities for things like sharing.

You end up hosting a bunch of disjointed and separate services. Sandstorm feels much more like hosting Google Docs and it's barely ever used support for third party apps/document types.

Sandstorm requires aggressive app packaging work but the payoff is significant: Apps do not have independent authentication at all, logging into Sandstorm gets you into all of your applications, and every file can be shared using the same process with other users or the public trivially.

In fact, because we break apps into "grains" or documents, we can do crazy things like allow you create Collections which comprise of documents made with different applications and then share that as a single unit with others. So I can take a couple specific Etherpad documents, a Wekan board, and a WordPress, put them into a project collection, and then share that with a collaborator with one link.