Re:
What your wife is complaining about is just an uncomfortable saddle and maybe a heavy bike. I don't think a retrobike would be a solution.
Although I also love retrobikes, I must admit one of the biggest improvements along the years has been in geometry. Today's bikes are way more comfortable while remaining nimble. Retrobikes are known for long top tubes, very long stems, and narrow handlebars that usually lay well below the saddle height. Not very female friendly.
My wife has a retrobike ('91 Trek 950) and a "modern" bike ('07 Trek 3700) and there is no doubt which one she'll pick. The modern bike has a wide riser bar, the stem is short and high leaving the handlebar at the same level as the saddle, the crappy suspension does the job in easy trails... Besides, many big brands know the lowest range is usually bought by beginners and they adapt the geometry accordingly.
To make the retrobike comfortable for her, I had to install a ridiculously tall and short stem, and that fixed the job for her, even if the bike looks ugly, while the modern one came "right" from the start while remaining off-road ready.
So although a new retro bike sounds like a great project for you, I'd recommend for your wife to get her a new saddle (probably wider since the high stem places most of her weight at the rear) and better components to lighten up the whole bike. Wider tyres to increase comfort, and done!
But this is just my opinion based only on personal experience...
