Recreational & Family - Feeling guilty

My wife, for very valid reasons, left the research for her first decent bike to me.

I narrowed it down to Trek 7100, Marin Kentfield, Specialized crossroads. All had Women Specific Design (WSD) variants, and we decided to not care about WSD, but buy the one that fits her best. I actually did not even look at the geometries to find the difference between the mens and the womens bikes.

And then, at the bike shop, I let us talked into buying a Trek 7200 FX, even though she was a little unsure about how comfortable the saddle was. Later, after comign back home, I looked up the specs, and the geometry is a trace different. In retrospect, the LBS probably did not have a WSD bike set up: the only WSD bike she tried there was a Trek 7000. I attributed the saddle discomfort to the fact that she was riding for the first time.

I dont have a specific question, and want to leave this open ended. Any experiences with the difference WSD makes? Any suggestions on how I can help her if she really finds the bike uncomfortable after extended riding? I would appreciate any help.

WSD is a shorter bike for the same "size", mostly in a shorter top tube. This is really needed more for smaller women.
The length of a bike determines how stretched out the rider is.
Many women have more leg than torso and can be very stretched out on "normal" bikes.
For fitness and riding around, the ideal riding position is likely to be somewhere between a racing crouch and a leisure riders upright position, ie a touring position with the back at about 45 degrees with flexed elbows and relaxed shoulders.

When setting up the bike position you fit the bike to the rider, not the other way round.
You start with setting the saddle relative to the pedals, then you set the bars relative to the saddle.
The bars can be above or below the saddle but level is a good starting point.

Have a read of
http://www.myra-simon.com/bike/womens-fit.html
and
www.peterwhitecycles.com/fitting.htm

Most discomfort on bikes can be traced to the saddle. If that's the source of the problem, simply replace it with a women's specific design (wider at the back for their wider sit bone placement). Assuming you bought her the right size frame, you should be able to swap components to make it perfect if the geometry is a bit off (you'd probably be making the same changes on the WSD model so don't think you are wasting money).