What stages do PCB mass-assembly techniques come in?
As Olin said, SMT is normally easier than TH.  I can solder SMT parts much better and faster (except for QFN's and BGA's, which I don't have the tools for).  

Much of the remainder of your question is highly dependent on the situation and opinion.  Let me give you some random data points for you to consider:


The company that I work has three PCB assembly lines.  For prototypes we often run about 12 PCB's in a batch.  But we have one assembly line that we call our "Build To Order" line, in which products are only built once they are ordered from the customer.  That line is setup to be economical just running a batch of a SINGLE PCB.
Prototype runs on some assembly lines is considered a dry-run for production.  So even if that run of boards is not cost effective in the short term, it might still need to be done to make sure that the assembly line is properly configured for volume production of that board.
Reflow ovens are the preferred method to solder SMT parts.  Wave soldering was preferred for TH parts.  But it is becoming increasingly popular to get rid of the wave soldering machines and do TH parts in a reflow oven.  This is done by putting enough paste down the hole.
Hand soldering, even in volume production, is sometimes required for difficult parts.  When this occurs, the other parts are normally soldered using the machines and only the difficult parts are hand soldered.  An example of this might be a large inductor that is right next to a BGA.  It could take a lot of heat to solder that inductor properly in an oven, enough heat to damage the BGA.  In that case, the inductor would be hand-stuffed.
The costs of a professional level SMT assembly line varies depending on speed, volume, accuracy (for small parts), etc.  I would guess you could do it for as little as US$100k, but $500k to more than $1 million is not uncommon.  Places that do a lot of BGAs usually have an X-Ray machine that could cost $750k all by itself.  
Most pick and place machines are separated into TH machines and SMT machines.  I'm sure there is something out there that can do them both, but I haven't seen one.  If you want to do them both, then you need two machines.
The best way to improve the efficiency of hand-soldering is to not do it.  Seriously!  Or to get things assembled in a country with very cheap labor.


The different levels of assembly are roughly this:


Hand assemble a circuit on perf-board.  Useful for making ONE unit, ever. 
Have the EE stuff a PCB by hand.  Useful for 1 or 2 units.
Have a technician stuff a PCB by hand.  Useful for 1 to 20 units, depending on the number of parts and the complexity. 
Stuff some parts by hand, some by machine.  Only useful if you can't do it all by machine. 
Do it all by machine.  Useful for 1 to 1,000,000+, depending on the complexity of the circuit and how the factory is setup.


It is hard to generalize about assembly methods and cost-effectiveness without considering the factory/company that will be doing the assembly.