I have had this same problem a while back. Unfortunately I think the answer is case by case, and I can't remember what exactly fixed it other than playing around with versions of MySQL Server and MySQL Connector/Net versions.
I have VS 2015 so I just tried to recreate this problem. I was unable to do so as I installed MySQL for VS 1.2.7 and Connector/Net 6.9.9 and was able to see MySQL Database as an option in the Data Sources window.
I recommend uninstalling both MySQL for VS and your Connector/Net 6.9.9 and then reinstalling them. Make sure you install MySQL for VS before Connector/Net as the documenation you linked in your question says "Always install MySQL for Visual Studio before installing MySQL Connector/Net."
You might also try using MySQL community server instead of MySQL for VS and using an older version of Connector/Net.
Update
Try doing the following:
- Uninstall MySQL for VS and Connector/Net.
- Install Connector/Net 6.9.9 by doing a custom installation. Remove the Web providers feature from the installation and continue with installation.
- Install MySQL for VS 1.2.7 by doing a custom installation. Make sure that the Visual Studio Integration feature is selected for installation and finish installation (It should be selected by default).
Update 2
If you want more alternatives to reinstalling:
Try checking out your machine.config file properties to see if the MySQL Data Provider property is similar to mine by going to C:\Windows\Microsoft.NET\Framework\v2.0.50727\CONFIG
Lines to check:
- ltsadd name="MySQL Data Provider" invariant="MySql.Data.MySqlClient" description=".Net Framework Data Provider for MySQL" type="MySql.Data.MySqlClient.MySqlClientFactory, MySql.Data, Version=6.9.9.0, Culture=neutral, PublicKeyToken=XXXXXXXXX" /gts
Also, maybe try a creating a website instead of a project or vice versa. There are multiple ways to get to the Data Source window. You could try creating an ADO.Net object and adding a connection to see if that data source window displays MySQL as a data source. You can also create a connection through the server explorer window. Just follow these steps.