I agree with @timday that you should reject your investigation to something โrealโ, and, as you suggested in the commentary, you might want the story to relate to a solution between a desktop or browser.
This is exactly what I'm working on right now. My client has a visualization application that currently runs on the Windows desktop. A typical scene for them has 500,000 triangles, lots of textures and transparency. Currently, their users are not inclined to install the viewer - they usually work in corporate environments where system administrators control what is installed on their computers. And several users would prefer to run visualization on their iPads, where the viewer will not work anyway. Therefore, my client wants to know whether WebGL will solve its platform problems - it does not matter that no browser officially supports WebGL, and that neither IE nor the iPad announced any support.
Remember that any benchmarks you make are relatively meaningless because you are measuring a moving target. Browser manufacturers are working hard to implement WebGL, and they update their beta version frequently. Not only do they work on implementing WebGL, but they have to worry about browser security issues and the overall pipeline flow. This video talks about some issues (and gives you an idea of โโwhat to watch). Additionally, performance may vary depending on your OS and graphics hardware.
As you pointed out, as soon as WebGL runs on graphics hardware, it should run as fast as a desktop application. Your tests should try to confirm this, and then you should try to measure where performance is lost as a result of being in the browser. I feel that Javascript itself is not a bottleneck, simply because there is not much Javascript to execute (and it's pretty fast these days). However, as described at the end of the aforementioned video, there may be inefficiencies that occur in Javascript-C ++ bindings, request validation, flow control, and what not. On the other hand, browser makers (at least Google) are working to smooth out these excesses.
One of the things I noticed is not frame rate / performance issues (in my current test, I can display 500,000 textured triangles at 30 frames per second), but these frameworks don't seem very consistent and these frames seem time discarded from time to time. I suspect, but I donโt know, whether this is due to the relatively simple setInterval() method or running the animation in Javascript. (Mozilla mozRequestAnimationFrame may be a way to handle this better).
Although I do not know how useful the above would be for your thesis, it seems to me that you have a rich topic, and you should do more than just write simple tests. Perhaps you should start with some tests, compare browser and desktop performance, and then try to learn best practices for not only the solution between the browser and the desktop, but also for writing WebGL applications.
There are many WebGL infrastructures. I tried a couple, and was very impressed - there is something to learn from them. Depending on your interests and requirements of the thesis, you may also be interested in a comparative analysis.
Be that as it may, I suspect that there is a large community of potential WebGL users who will starve for the information you are about to research.