I'll try and explain my point of view. A lot of it is based on the ending of the game and how that colours the rest of the story, so if you don't want spoilers then please skip this post.
Please note a couple of things before reading:
1. it's totally okay if the story didn't come across to you that way. If you enjoyed the story and I didn't then, well, it sounds like you got the better end of the bargain, right?
On the other side of the coin, how the story came across to me doesn't mean I viewed it "wrong" - how I felt is how I felt.
2. the story is probably a lot better if you never played Starcraft, and in particular Brood War. That is because Chris Metzen has learned somewhere along the way that retconning beloved universes to fit whatever story takes your fancy this year is a good thing. This had good results in Warcraft 3 (and the foreward to the Warcraft Archive talks about how Richard A. Knaak phoned Metzen one day with a really awesome idea for a retcon, so that might be where it all began) but the same attitude has carried over to WoW, Starcraft 2 and Diablo 3, with what I'd argue are bad results.
So, to start off with some essential background: in the original Starcraft, there was no big romance between Raynor and Kerrigan. They actually get off to a pretty bad start and maintain a respectful distance from then on, which isn't super long because Kerrigan gets captured by the Zerg (though you don't know this at the time) on level 8 or so. Later, in the Zerg campaign, she turns out to be the Overmind's grand new creation and becomes Infested Kerrigan.
A bunch of things happen and the Overmind dies. Infested Kerrigan turns into the Queen of Blades we all know and love. The United Earth Directorate turns up and some bizarre teaming up with Kerrigan against them ensues, surprisingly enough followed by her stabbing her allies in the back to great effect. Part of the stabbing in the back involves her cheesing Fenix with Spawn Broodling, which is like the complete opposite of the glorious death in battle the Khala demands. Raynor is
super mad at this, not so much because he's into the Khala but because Fenix is his best friend. He follows this by declaring that whatever humanity was left in Kerrigan is long gone and that one day - maybe not soon, on account of just having had his entire army trashed by her sudden but inevitable betrayal, but one day - he will find and kill her.
Yeah.
So anyway, with that brief summation out of the way we come to Starcraft 2. Right at the start of the game we see Raynor looking wistfully at his photo of Kerrigan, not with the sadness of murderous intent too long denied but with the sad reminiscence of, perhaps, love long lost. Oh oh, we're off to a bad start here.
I'd like to derail slightly to talk about a bit of a problem with Raynor's characterisation throughout the story. At the start of the game, we're presented with the marketing-friendly line, "It's time to kick this revolution into overdrive!" And Raynor certainly delivers on that pretty well, succeeding in everything he attempts to do from that point onwards. The problem is, after that he frequently ends up in cutscenes moping about how nothing is going their way and life's not fair and nobody even
commented on his last livejournal post and so on (full disclosure: I have a livejournal). His negative attitude really clashes badly with the continual success he meets and makes his characterisation appear a bit incoherent.
So throughout the story we meet with Kerrigan. Part of the problem with Kerrigan is she seems very... listless. Passive. She doesn't really seem to ever do anything, and the few things she halfheartedly attempts (with what's presumably still the most fearsome force in the Koprulu sector) are easily thwarted by the plucky Raynor and his motley band.
Let's skip over the rest of the game, since it's really pretty random for the most part. At Char, we're also presented with some weird stuff. The Confederate fleet launches a frontal assault. To recap, this is the same Confederacy that had its entire fleet destroyed, followed by Arcturus Mengsk putting together a fleet of whatever random ships he could find - mostly privately-owned ones - and then getting
that destroyed, too. Maybe doomsday fleets just come in cereal boxes in the future (but not Zerg cereal boxes, apparently).
This fleet manages to break into Char and Kerrigan, powerless to do anything but run into your entrenched defenses of lots of whatever it is you brought over and over, is defeated and turned into naked human Kerrigan. Raynor kills his new old best friend and walks off into the sunset in his chunky power armour with the naked Kerrigan.
So when I say depowering and objectifying, I'd be talking about this iconic female character who's repeatedly shown to be ineffective, who ends up stripped of her power (and clothes) against her will and carried away as a prize by the male lead.
What makes the whole thing even more tragic is how much stronger the story and characters (especially Raynor's) could be without the love story retcon. When Zeratul reveals to Raynor that Kerrigan needs to be saved to save the galaxy, that could have been a powerful moment - he suddenly finds himself needing to help the woman he's sworn to kill. Instead, it's turned into an excuse for Raynor to do what he wants to do anyway - save his girlfriend - and is completely robbed of any emotional impact.
It's a real shame.