True there are tons of low cost needy kittens in shelters, not usually free but almost free some locations. Here in San Francisco I think it is ~$200 (we paid $180 14 years ago to adopt a feral kitten here). BUT there aren't tons of Savannahs out there in shelters. The reason you pay the money is because you are focused on a specific breed, that has been selected for characteristics. You want a certain look or a certain type of cat. In the Savannah's case you want an elegant athletic look and you like a high energy interactive cat. That's not so easy to walk into a shelter and find.
The more expensive kittens from the better type of breeder are not necessarily likely to come with as many medical issues. The lines are well-researched, many breeders screen for HCM and although screening isn't a perfect method when you have 3 or 4 generations of screened cats you can feel a little safer about heart disease. That and looking for structurally sound cats, and culling out the cats that produce problems. A cut-price breeder is probably more inclined to keep breeding a cat that is producing defects than a breeder that prides themselves on the quality of their kittens.
We all choose where to spend our money. I think when you average out the purchase price over the lifetime of the cat... and balance against the joy it brings...then $5K is not that outrageous. But only if you have that money to spend, and not everyone can. Wanting an F2 for $2K is very much champagne taste on a beer budget. I would think it more sane to be looking for the best F4-F5 and you may find you get an amazing cat for that. I would pit the intelligence of my current F5 kittens against an F1 btw...I have both in my household. My F5s descend from my original F2 female and she was the smartest of cats...but her progeny and grandprogeny inherited that from her and remind us of her every day. You can find the looks and the personality at F4 level, you just have to be more selective and it might take more time to find.
