We didn't pay for the TICA paperwork, and he is not neutered. He was sold to us as a F3.
His birthday is April 28, 2016. We took him to the vet last Friday, and he weighed 2.5 lbs (@ 8 weeks & 1 day old).
It costs a tiny amount to register a litter of kittens hence the paperwork should not be something that is withheld. Some breeders might hold papers until proof of spay/neuter (if they don't spay/neuter before the kitten leaves), but there is no reason to not give papers to you if the parents of your kitten are registered.
Not only is it proof of what you purchased, as you now have doubts given your vet's reaction, but it can be important if your state or county decides to pass regulations only allowing a certain generation or further, you may need to prove what you have!
I would go back to the breeder and ask for papers. Hopefully this is just an omission and you can get the papers now.
I do think from those pictures that you do have a Savannah kitten, BUT I also see what your vet is seeing. It comes from the Savannah breed still being relatively young, the effect of the outcross breeds used in breed development can still sometimes be seen, and in some cases quite strongly. There is obviously Bengal heritage in your Savannah kitten. Don't worry, probably ~90% or more of our Savannahs have "some" Bengal in their pedigrees, if you dig far enough. It's possible that it is more recent with your kitten or he just got a bigger dose (you know how a kid sometimes looks more like a grandparent than they look like their parent?).
When the breeder said the kitten is F3 did they give an A, B or C after that? Do you know if daddy was a Savannah too, or might he be Bengal. Does the breeder also breed Bengals?