I have to say I find the rust issue of Fats slightly funny, sealed tubes, with lip seals on seat collars and taped shut slots on seat tubes. They put a little more effort into rust prevention than Kona, Specialized and the like.
Like any bike its up to the owner to ensure the seat tube is kept in tip top condition, and every type of frame suffers internal seat tube problems if not regularly cleaned and maintained.
As for rusting thru, the only frame I have this happen to was an abused steel Stumpjumper, and it had a lifetime warranty anyway.
Alloy frames, (even Kleins) may have a limited fatigue life in comparison to steel and titanium, depending on use, but rarely enough to cause problems later on in life unless very very light weight.
Most problems boil down to two things, poor manufacture or neglectful owners.
As for pricing, well I think most Retro stuff is a little overpriced and less use on most of today's developed trails, there is no doubt suspension is better as are disc brakes.
But, these days components are not as nice, there is little pride in owning today's "bling" as it is poorly manufactured. And most modern group-sets are pathetically manufactured and finished by comparison to stuff from the 90's. Many bikes these days also have pathetic geometry, designed around the suspension and not the rider.
Today's bikes are about fashion and profit, not pride of ownership and skilled manufacture. Just take a look at a pre Trek Klein, or a Sandvik Ti frame, a steel Serotta or Fat in comparison to any of today's bike frames, look at how poor Trek Kleins were in comparison, comparable to when Specialized dropped M2 ceramic matrix frames for hyped alloy M4 rubbish.
