Planes are certified by their "type", which is a document describing in official terms what the airplane is. For larger aircraft, the pilot is required to obtain a "type rating" which trains the pilot on all of the special ways in which an airplane of that type must be flown. So, as long as the aircraft conforms to the type certificate, theoretically no further training is required.
This leads to the manufacturers and airlines to buy new aircraft that conform to the old type certificate, as it means the pilots don't have to be retrained. Southwest is a perfect example of this, in that they are flying planes that use the same certificate as the 737s they were flying when the company was formed (ignoring the 727s that Southwest was flying at the very beginning).
It's an all-or-nothing situation. Either the plane conforms to the type certificate exactly, and no training is required, or it requires a completely new type certificate, and all pilots will need to obtain a new type rating. So, we can bash Boeing, but the reality is we're in this situation because the airlines want this as well (to avoid the retraining issue), and are pushed into the current situation due to the all-or-nothing nature of the type cert.
The idea that type certificates would have a life across many generations of aircraft was likely not considered when the system was established in the first place. Something like a sub-type might work as an enhancement, where the training to fly a modified aircraft is much less involved than a full type rating. Pilots are training all the time anyway, so it seems feasible that simply allowing for a training session on "here's what you need to know about this new aircraft" could easily be incorporated into the training cycle.
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