1. Their package/plugin system sucks (last I tried it anyway). It basically just seems to download a bunch of junk files for every plugin without any intelligence, and if the package updates you have a big mess on your hands, trying to combine your app code with the newest plugin code.
2. You are pretty much forced to use C#, even though the company has more money than god and could easily fund grants to allow for great variety of language options. By siloing themselves within the C# ecosystem, they will likely never have an ecosystem of third party development tools that could improve the lives of their users.