The Savage 99 required a lot of hand fitting of parts, and that made the cost of production so high that the profit margins became too small to sustain the model in the lineup.
When the competition can sell a gun for 80% of your retail price, that performs as well as your product, you have to reduce your production costs. That is why the quality fell off over the last decade of production; Savage was trying to keep the 99 alive - they even had them manufactured overseas in an effort to reduce the cost to a point where they could make a profit at the market price the competition set.
As the quality dropped, so did the demand, and the 99 was eliminated due to market forces. The Savage 99 would probably cost $2000 to produce today with decent quality, and not many hunters want to pay that much for a deer, elk or bear hunting gun.
The design is generally not capable of the accuracy most people expect today - My model 99 in .308Win will shoot into a 1.5 inch group at 100 yards, using a solid bench rest and a 6 power scope, but that may be the exception rather than the rule when it comes to accuracy of the model 99.
If I had $750 to spend on a hunting rifle, and I knew that rifle was capable of 1.5 inch groups at 100 yards using standard factory ammo in several different loads, I would then consider other characteristics of the rifle. Style, weight, handiness, fit to the shooter, quality and reliability of the gun, reputation and service record of the manufacturer, etc. I like the Savage model 99; it feels good, balances well, fits me well. I would gladly pay $750 for a new Savage model 99 in a different hunting caliber, provided the accuracy, reliability and quality were on par with other rifles available on the market.
I do not think that Savage can actually make and sell the model 99 at a competitive price. That means that people that want to use them will buy used from previous owners, and they are now collectors items, so the prices of used guns are climbing above the level most hunters are willing to pay for a gun that will get wet, scratched and banged around in the field.