I honestly have not read the third, but have read enough here and other places to know that there are significant differences. I think many of the change were made not based on scientific studies, but rather in response to criticisms, to incorporate approaches that are more popular these days than when he wrote his initial editions, and, frankly, to justify a third edition so he could sell more books.
Among the changes:
- no more table for longer tempo runs;
- an increased emphasis on cruise intervals over straight tempo runs;
- the addition of marathon pace runs into plans for shorter distance races;
- the inclusion of back to back workouts.
He does address some of these concepts in his prior edition, but there seems to be a change of emphasis on those things. For example, while he said both cruise intervals and tempo runs are equally effective physiologically, he seemed to really advocate for the 20 minute tempo run in the 2nd edition based on the idea that it required greater mental focus that would have race day benefits. I think he now probably leans toward cruise intervals because they feel less stressful. Similarly, he hit on back-to-backs in the 2nd, but really didn't emphasize them.
Other things are just plain contrary to what he previously said. For example, he basically said in the second edition that marathon paced runs do nothing for you physiologically and he only included them in M training plans for purposes of locking into race pace and some sort of amorphous mental toughness concept. He now includes them in most training plans.