He was a tragic antihero in some sense - as you, the player, are chosen by him and Reshiram to fight him, so too was he chosen by Ghetsis to be brainwashed and raised in such a way that would make him dedicated to the advancement of Team Plasma.
Unlike Archie and Maxxie, because we saw so much of him, his realisation that maybe his goals aren't perfect, was a lot more believable. The way he's incredibly friendly to the player too helps you to like him, he's nicer to the player than Silver in HgSs ever is. His funny way of talking, and the fact that he releases his pokémon back into their habitats (I always assumed this, before B2W2 came out) when he's done, he's just so damn likeable!
As an aside, that final showdown is the most epic moment in pokémon, finally beating out Rayquaza's arrival in Sootopolis City for me (stupid weather and the fact that barely anyone would know kinda kept battling Red out of the running imo). It also really formed my opinions on Reshiram and Zekrom. Between Zekrom's first appearance in Dragonspiral Tower, his dramatic entrance in the Plasma Castle, and then having to face him in what you believe is the final battle (let's be honest it is the climactic battle of the story, but you then have to defeat Ghetsis straight after which is just as important), I really see Zekrom as the bad guy out of the two dragons. The colouring doesn't help, Reshiram just looks so noble coming to the rescue like that, but still. They're meant to be conflictin opinions, neither of which is right, yet Zekrom to me seems to be a bad guy despite not being allied with one.