The biggest problem with Daniels is he helped make American running for a long time obsessed with a training-zone model. I do like how he allows individualization in his program (as any should), but he really does neglect a lot of other things.For instance, if I wished to run 10k his plan would focus on threshold and VO2 stuff. His I-run paces are ~3k-5k pace and doesn't serve a runner trying to get used to their 10k racing rhythm. That work is IMPORTANT, but not as important as the paces you will be running for your race. Daniels assumes that the treshold stuff (crusie intevals, tempos, etc.) would help fill in the gap. What is missing is that race specific speed. You see a lot more of this specificity with Canova and some of the other coaches who have came into the limelight recently.
That is just one example of why the training zone models can be a little screwy. You neglect that "gray area" of training that a lot of coaches consider junk. Sometimes that training is very important in accomplishing what you want to do for your race. His Marathon Pace stuff for example: I agree with you that he probably didn't initially find any value in that stuff (E running/T running covers it in his eyes) and recently added it in wake of other coaches rediscovering its value in a training program. For him, this was once a training zone that wasn't notable at all. Now it is. Glad he updated it, but there are plenty of other stuff he is missing out on. (btw...short alactic hill sprints? steady state running? etc.). If people are able to look through his book and say that he really does advocate some of this stuff, it isn't as obvious as it needs to be for people.
P.S. I am not saying he is a bad coach. He did a lot for American distance running with a focus on tempo running, light speed work year round, etc.