I want to have a thesis that is related to games but I don't know where to focus that will really have a big attraction on our computer department. Most of the thesis that was presented are only in 2D using C# with XNA but there are also some who use 3D with C++. So, I think making my game uin 3D and C++ would be a big plus. I posted here to gather many suggestion and advice for my thesis project. So where do you think should I focus? Gameplay, graphics or what?

Your question is very general, and that's probably something that you or your department should answer?

If you focused on gameplay what would you focus on?

Suggestions (from a college drop out)
AI:
* dynamic behavior
* immersion
* connecting subcontiously with the player

Performance:
* physics
* networking
* utilizing SPU's / mulit cores / distributed computing

Graphics:
* efficiency
* realism

Novelty:
* FEA
* Fluids
* Atmospheric dynamics
* Weather / ocean simulation

do you have any more specifications?

I don't have any thesis right now but next term I have. Most of my friends in the upperclass told me that I should think of a topic that is unique for my thesis project. So I came here and posted to ask for suggestion and advice on which part is better to focus? gameplay or the graphics? I'm a BS computer science student, though.

It doesn't matter if you focus on gameplay or graphics provided that you focus on something unique.
And don't go and write an entire game just to show off your thesis idea as it will be wasted effort. You'll only be marked on the section relevent to your thesis. It's much better to use an open sourced game and then apply your thesis to that.
For example say you wanted to write your thesis about goal oriented action planing there is no point wring a whole game as you'd spend more time developing the game than you would actually studying the AI and when marking it your 3D graphics engine, sound, networking and everything else will be ignored as it isn't even relavent to your thesis.