Heart of the Swarm: I finished this awhile back, though still doing some achievement grinding (I better not have to replay the entire campaign to get the Kerrigan level 70 achievement after I somehow got cheesed out of a level on "Supreme," sigh.) I'm mostly of the Ephraim/Laggy "plot so bad" school of thought, BUT. The plot is still fun anyway. I mean Diablo games all have an objectively horrible plot, but Blizzard pulls it off stylishly, so whatever.
Anyway, if the plot is viewed with SRS BIZNESS googles, the biggest problem is that the game doesn't want Kerrigan to be a villain this time around. Now, it's very possible that a plot could have been written that sold Kerrigan-the-reformed-hero, but it'd have to really put a new spin on the Zerg, who have a bunch of, well, evil stuff in their arsenal, infestation being the most obvious, but the general galaxy-domination-via-killing-everyone also pretty bad. The WC3 Orcs were closer: they went from worshippers of demons from beyond to shamanistic honorable-war-is-cool or something, which is fine for a fantasy universe. But no, the story simultaneously wants us to be sympathetic for Kerrigan - she's the good girl, Mengsk is allied with the hybrids which are just inherently Evil, Because - yet still let Kerrigan do all sorts of super-evil shit and act casual. Even if we seriously believe that Kerrigan is avoiding civilian populations on Korhal or some crap, and if we grant that because this is an SRPG Kerrigan's best way to get at Mengsk involves attacking the Dominion (rather than being a freakin' UNSTOPPABLE INVISIBLE PSIONIC ASSASSIN like she kind of is and trying to kill Mengsk Solid Snake style) - you do crap like infest random prisoners or barracks staff into an unstoppable wave of infested! I'm pretty sure I remember how the whole colonist plotline in Wings of Liberty went, making people go batshit and kill their friends seems pretty unforgiveable. And Kerrigan is busy sending off the other broodmothers to attack random other Dominion worlds, which I'm sure will be done with the greatest of care after how Niadra reacts to similar orders from Kerrigan! (read: set up some Zerg to knock down at the start of Legacy of the Void before the big Amon showdown.) Anyway, yeah, I just don't buy Kerrigan the hero, and I'm surprised Raynor buys it at the end, either. She already did the "oh I was being mind controlled by the Overmind I'm not really evil" act before turning around and murdering everyone act once in SC:BW, and Raynor even briefly mentions it in "what about Fenix," so even if she really WAS good, everyone should be rolling their eyes and playing with the fact that she can't possibly sell this after fooling everyonce once already.
If they'd decided to spit on Wings of Liberty in a different way, they should have just had Kerrigan been evil, and skipped having her transform at all. Raynor was a fool to think that a magic wand would untwist her; she's a psychotic nut bent on not just killing Mengsk, but dominating the galaxy with all bowing to her. You don't need to look all Zergy to be a monster! THen at least the story wouldn't need the bizarre contortions it goes into to explain why Kerrigan taking control of the Zerg, and all the bad things she does, are really all about her pinpoint revenge against Mengsk & his cronies, with totally no innocents swept up in the mess, nope. (Okay, the game does kind of hit it in the first Protoss colony mission on the ice planet, but I'm not sure WTF Kerrigan was even doing there or why she cared or why she thinks that the Protoss won't find out soon enough anyway, so while I appreciate sticking some innocents in Kerrigan's line of fire and owning those deaths, it's still incoherent and the game still thinks Kerrigan is a hero anyway.)
Also, I'm hardly a crazed SC1 fanboy, having played its campaign long after the game came out (2002 or so?) and far preferring Myth: The Fallen Lords for my 1997 RTS fix, which also has a way better done plotline. SC1 plot: Not actually that amazing, but it's competent. Wings of Liberty is my favorite SC plotline so far, for all that Blizzard picked a lame direction to afterward and the Xel'Naga artifact plot was pretty weak.