The other two possibilities (assuming we can rule out viruses/spyware and disk fragmentation - yes that means go ahead and run your virus scan and defragment your drive now if you haven't) will hopefully be diagnosed by thoroughly anolyzing every aspect of your system's performance using the following tools. This should allow us to determine if some seemingly obscure and very specific task is being performed significantly slowly compared to the rest of your results. If, by this point, you have exhausted every imaginable way of manually tweaking the game itself then there is a strong possibility that this one (or possibly several) tasks are also one that Fallout: New Vegas performs very often.
Once we know if your system is having an unusually hard time with some specific function then it is easy to suggest settings changes, firmware updates, or software that may be misbehaving despite being perfectly non-malicious. With luck I (and the rest of the helpful geeks on here) will be able to provide some simple fixes to try and then you will be able to enjoy the game as you thought you would.
If there are no unusual deficiencies in your system performance, an your system is decidedly powerful enough to run the game well, and there is no potentially badly behaved software running then we are still closer to solving your problem. If that is the case then we can be relatively confident that it is a compatibility issue between some aspect of the modified Gamebryo engine, the games content (textures, filters, sound files), and your particular hardware setup. Though that doesn't help you immediately, it will help bethesda or potentially the mod community develop fixes; getting the hardware configurations of people who have otherwise unexplainable poor performance we will be able to help determine which devices Bethesda and modders may need to improve performance with.
Do the following:
(1) Describe your performance issue
Explain in what way the game is running poorly. It might sound silly, but knowing how, where, and when it is running poorly is much more helpful than that you have a low frame rate. If your performance is always roughly equally bad then many of the first questions here will be "no, it's always bad"- sorry about that.
-Unless the performance is simply ALWAYS poor- when, in game, do you notice poor performance?
-Does it happen when you do something specific, in specific areas, around certain NPCs or groups of NPCs?
-When performance is ppor does it eventually improve (and perhaps get worse again later) or does it not improve
again unless you exit and re-launch the game?
-Does the slow-down usually or always precede a crash? If it does, does it give you an error message, crash to
desktop with no error message, or freeze and become unresponsive?
-Alternatively, if the game does not crash shortly after startup or shortly after slowdown - does performance
get increasingly slow/clunky the longer you play?
-In what ways is it poor exactly? For example is the framerate simply very low, does the game run is spurts
of smooth movement and stuttering, do NPCs appear to teleport or slide instead of walking?
-How bad is it? If you are able to bring up the command console (hit tilde) you can use the TDT command to
display framerate.
-Does anything strange seem to happen as well as the slow down? Yeah that's a very open question, but if
it seems weird maybe it is
(2) DxDiag
List your hardware configuration by posting your dxdiag.txt contents. Please pot the "spoiler" tag around it so that it does not take up several pages worth of screen space. The file should contain enough about your hardware for us to refer to while helping you. We can always ask for more specifics if we need to.
(2) Try running the following tools (just the free versions):
http://www.sisoftware.net/?d=&f=downandbuy&l=en&a=
http://www.futuremark.com/benchmarks/(also 3D mark if you want- their site may be able to help you figure out what your performance SHOULD be)
http://www.hdtune.com/download.html (Just the free version, though there's a free trial for the pro as well)
On one of my systems (old now, but was high-end enough at the time to expect good performance) those tools were able to help me diagnose that the hard-disk my games were installed on had been semi-permanently set to PIO mode by Windows. The disk was fine, but there had been enough read/write errors over the life of the drive (I think 5 is the magic number) for windows to decide to set it to the slowest possible mode and never have it revert. The fix for that was a registry hack that tricked Windows into thinking the drive had been plugged in for the first time - wiping the slate. A year and a half later it had not reverted so obviously Windows decision to sacrifice massive amounts of performance to protect my data was both paternalistic and incredibly soul-killingly stupid.
If those utilities point out any area of low performance, or if you spot something that is relatively low yourself, make a note of it. If have online photo storage, go ahead and post a screenshot of the failed test. If everything benchmarks well or at least similarly well then note that - also provide your scores from PC Mark or SiSoft Sandra.
(3) Post
Post what you have found - be sure to put "[spoiler]" tages around any long lists/ouput text you paste in your post so it's easier to read everything. Spoiler tags are used just like the formatting, link, and quote tags they go in brackets like "[" and you use "spoiler" before the text you want to hide and "/spoiler" after it.
If you have any questions or want to suggest other steps please post that too. I will try to help as often as possible and check this thread regularly. Anyone who consideres themselves geek enough should feel free to pitch in too.