While I can understand the sentiment, what Thunder does is make things easier (sometimes much easier). All of that can still be done in other ways without Thunder (at least everything I have tried to do). I have used a lot of different CMSs over the years, including SharePoint and DNN. This is by far my favorite to work on. Even without Thunder, most of it is much easier for me to accomplish than what I had to go through with the others.
I do think that they need to do a better job of how to do things both with and without Thunder - i.e. have a section for both on the same page where appropriate. Not only would it help those with the problem we have both experienced, it would help everyone understand what is going on under the hood and make us better SF devs.
I also think it would be good for them to develop a lightweight stand alone tool that can use Thunder outside of Visual Studio, again for people experiencing the issue.
Finally, they really should start working on the new version of VS's Thunder as soon as is practical, instead of waiting until after the RTM (at least it appears that way from the outside). Thunder should be ready to go right out of the box when a new version of VS is released, and I believe VS 2015 took way too long.