So, I'm doing a completely modded playthrough of Fallout 3. It is the GOTY and has all the DLC's. So is Project Reality better or is Fellout with Enhanced Weather?

Depends on your preference, I personally like Project Reality more than Fellout.
I suggest trying them both to find out for yourself.

Fellout is good for fallout 3 and PR is good for NV. But I don't think fellout would be a thing in Fallout 4 cause all fellout did was getting rid of the tint in the skys. Which fallout 4 deosn't have. On the other hand PR sets the right tone for the weather you want.

Project reality just kills your framerate, Fellout messes up your lighting sometimes if you uninstall it.