I think Bakula's best moments were when he had to silently show Archer's internal struggles when faced with difficult decisions. He was always good at tortured soul type characters. The dialogue he had to deliver was the weak spot. He'd probably make an excellent villain.
This brings up something I have felt since the show was on, that TPTB should have cut down on Scott's dialogue similar to what was done with Admiral Adama in BSG.
If Archer had been modeled after say, the character Kevin Costner played in "Open Range", he may have had an easier time performing the role and Archer might have been more intriguing if not more likable to the fans. Scott seems well suited to play "the quiet man", creating anticipation and tension for his dialogue, thereby kind of manufacturing a form of "charisma".
Truth be told, I really didn't "dislike" Archer, I was pretty ambivalent about the character -- I just disliked the way Scott played him.