Season 3 put him in a completely different situation. Arguably more pressure than any other Star Trek Captain has ever faced. Singularly charged with saving humanity? ... with no help??? I can understand the pressure and how that burden kept pressing and pressing. He didn't need to act like a tough guy to be the tough guy. When he did, it did not resonate well with me.
This is where I'll address Scott's acting a little. From chewing butt in his Cabin, to the mirror universe, etc.... he does not do "mad" or "angry" very well. I don't think it's in him. I can understand the story put the character in situations where that reaction was appropriate, but he just doesn't play that part very well...
I agree with this. Bakula is a fine actor, but his range only goes so far when it comes to being angry. He's more convincing when he quietly simmers rather than rants.
Otherwise, I thought the character of Archer was appropriate for ENT and I thought one of his defining moments was in season four's "Home" when he finally faced all that he had been through in first three seasons:
"I lost something out there, and I don't know how to get it back."
--Captain Jonathan Archer
Archer went in as an eager (if not slightly na´ve) explorer not really knowing what he was in for and, IMO, that was befitting the series. He made mistakes, compromised some of his values, and had to take a long look at himself afterward and reevaluate. I do think that after his "trial by fire" in the first three seasons, Archer was of course a better captain. It could definitely be said that later captains benefited from lessons learned by Archer.