Season 3 The relationship with Peyton was inappropriate. I would have seen rather more action. Season 7 was OK. Only Jo had only always your coffee cup in the hand. instead of to work. And Mac has worked not enough in the laboratory. Too many Scenen with Jo.
I agree. I'd add 'Death House',and 'Uncertainty Rules' as stand-out episodes to the ones you mentioned, and there are a couple of other eps with some Mac scenes I really like (i.e. The Formula) or which I like because they allow us to see lesser-used characters get a bit more focus and see them in a different light (like Sid in 'Flag on the Play') but generally I watch the eps for Mac and Flack alone. There were also a couple of eps I really, really dislike such as 'RIP Marina Garitio' (although I like the Mac/Aubrey scenes in it) and 'Vacation Getaway' (which despite having worked my way through my s6 DVD set I still can't bring myself to rewatch) and 'It Happened to Me'.
I chose seasons 4 and 5 because they were the start of that Titanic sized disater known as D/L being shoved down our throats every single episode.
Season 6 was by the far the worst. The storylines and scripts for most of the episodes were simply dreadful. Towards the end the storys picked up but too little too late for season 6 as a whole.