Make sure you have 1.05 installed before proceeding. I guess it doesn't matter but your gimping yourself.
In-game Anti- Aliasing is broken. Game has pretty bad optimization/performance in a lot of ways. So by using the AA which does nothing you can be hurting yourself even more so.
Install InjectSMAA LINK HERE + GUIDE HERE
Go to.. C:\Users\....\Documents\my games\Far Cry 3\GamerProfile.xml
Use my settings[If you want] which effectively removes all the extreme performance demanding features AA[FXAA/MSAA]/Depth of Field/SSAO/SDSM. Everything else is MAXED.*Change resolution accordingly.*FILE HERE.
If you want to do it yourself.
Make sure your config says MSAALevel="0" AlphaToCoverage="0" SSAOLevel="0" SDSM="0"
MSAA/ALPHA should be off regardless. They offer little and take too much.
SSAO is optional, if you want on set to 6. Anything less looks pretty bad [like UDK SSAO].
SDSM is high qualitity sky, if you want on set to 1.
Depth of field/Motion Blur/FXAA off is you do the following..
Paste this after </CustomQuality>
<quality GameDepthOfField="0" CinematicDepthOfField="0" FXAALevel="0" CloudShadows="1" MotionBlur="0" id="ultrahigh"/>
If you are happy with how it is leave it but if performance is good and want more AA continue to Step two.
Use Nvidia Inspector. Use These settings.
It will eat ALOT of performance. Either reduce to 2x instead of 4x on each or unfortunately can't use. If playing at low resolution I highly recommend reducing injectSMAA setting/in-game graphical setting. Game is very jagged and 2xMS 2xSGSS makes it pretty sharp even at 720P. Can try to disable SGSS and just use 2XMS but I didn't test.