I liked all the Captain's...
The obvious answer would be Archer, because its easy to say, since many Trek fans didn't get into ENT as much as others (like myself did), first and foremost, Scott Bakula is an excellent actor, nobody can deny that, in the late 80's early 90's he was the face of Sci-Fi over on NBC (Quantum Leap, which he won a Golden Globe for and four Emmy nominations) Bakula excels at character acting and has a background in Broadway Productions and the Theatre..anyway
What most people don't like about Archer is the "Untrekness" of the character..bear in mind that ENT is set in the 22nd Century, before anything outside of our Solar System has been explored and Earth is still ironing out issues left over from WW III...Archer is eager to explore, he has no real experience with Alien Cultures (except the Vulcans), his ship hasn't been fully outfitted, his "Vulcan" initially annoys him and acts as a chaperone and his senior officers are just as inexperienced...in fact the Doctor knows more about Alien Cultures than probably the entirety of Starfleet Command
What Archer "Characterises" is a completely new form of "Captaincy", so far removed from the likes of Kirk, Picard, Sisko and Janeway, that its enough to turn core Trek fans away..however if you give the show a chance and watch the development of Archer, you'll see familiar qualities start to emerge and in the continunity of Trek, these qualities became the model of a Starfleet Officer later in the series..
Essentially what i'm getting at is I like Archer, he brought a sense of realism to the show that wasn't so far removed from 21st Century Culture (do you really think that 150 years later and a 3rd World War, we're gonna be perfect?!)
As for least favourite Captain, i'm going to have to say TOS Kirk....let me explain, In TOS, Kirk is the emobodiement of 1960's Television "Hero", he's a shallow, one sided and predictable character, however that being said, the TOS Movies Kirk, became one of my favourites, beginning in 1979 and refined greatly in 1982 a new Kirk emerged, one with so much depth it was hard to believe that this was the same character that graced the screens of a 1960's production, we found out numerous things about Kirk,
*He persuaded Starfleet to give him back the Enterprise and in the process shatter the dreams of its newest Captain
*He cheated in a Major Exam
*He has a Son, who he has never been involved with
*He doesn't get on well with "Ageing"
*Him and Spock are much closer than could be portrayed in a "campy" 1960's tv show (no slash comments, i'm talking about friendship here, brothers from other mothers and all that)
*He defies orders, steals the Enterprise and rescues Spock
*He essentially murders a Klingon crew (although this was a last resort, kill or be killed situation, he even offered to rescue their Captain)
*His ongoing hatred of Klingons and what they stand for, even showing reluctance to be a major part of a crucial diplomatic mission(as a result of them murdering his son in cold blood)
Things like this added so much more depth to the Kirk character, its amazing looking back at TOS and thinking "how did this guy become that guy?!"