I just don't understand why you do the 20 minute run in W5R3 but then back to shorter runs in week 6?
Why is W5R3 longer than W6R1?: I just don't... - Couch to 5K
having done wk5r3 on Monday and wk6r1 today I can tell you I'm thankful for the arrangement! There is some evidence that to build up stamina you need a mixture of long(er) and short(er) runs. By the time you get to W6r3 you are doing another long run and the two previous shorter ones are very helpful for building stamina again.
I think its so you dont get too confident & get yourself an injury. most books will tell you not to up speed or distance by more than 10% a week so going back to intervals makes sense to me ~ not just that wk5r3 was the first time you really asked your body to do that much in one go so enjoy the intervals as its only a couple of weeks where you wont be rewarded with a quick break I personally found wk6r1 one of the most hardest after that first week. good luck.
I completed wk5r3 on Tues without any major problems, could have gone on in fact. Today I did w6r1 and boy was it a different story. 8 mins seemed like an eternity!!! Ok so the high humidity was a factor but it seemed more a psychological struggle for some reason. Not sure why as like you I'd expected to be able to keep running 20 mins without a problem - maybe some people do. If I'd been asked to run 20 today I'd have been demoralised and downhearted.
It has given me even more faith in the programme - Laura obviously knows me better than I know myself!!