Breadboard/veroboard and SMT
First off, through hole components are far from gone. Even some of the more complicated microcontrollers still have through hole versions available, specifically for the purposes of quick prototyping. The through hole version go away when you start getting into speeds that just can't be done with through hole.

As far as prototyping with SMD, it really is not as bad as you seem to think it is. In about a week of practicing soldering surface mount components, I was able to remove and add SMD parts quickly with hand soldering (and I wouldn't consider myself great at soldering). This means that when you get a prototype you can fairly easily swap components out. And if you find that you have your circuit wrong, as far as connecting a trace to the wrong location, it is fairly simple to use a razor blade to cut a trace and then solder wire to jump to the correct place.

As far as the cost, prototype PCBs aren't that expensive either. Many people are able to make them at home now. Even when you send out for one, there are places that you can get a professional style 2 layer board for $33 or can get a board with out plated through holes and solder mask for cheaper.

What I have found is that for prototypes of any amount of value, as in will do more then flashing an LED or something, the problems that people run into with breadboards tends to be things like plugging a wire into the wrong row, or accidentally pulling a wire out while trying to do something. All of those things go away with PCBs resulting in it being much easier to focus on the prototype.