-Why don't marines need to reload? In the cut scenes (since SC1) they have had to.
The C-14 has a lot of ammo, since it's carried by a soldier in a combat armor, the rifle is big, the clips are big and, through they are pretty big for needles, the ammo is small compared to the clip size. a C-14 is more like a MachineGun than a common rifle. The powered armor helps compensate the recoil. They reload in cutscenes for dramatical reasons.
-Why don't any Terran units run out of ammo?
Already explained. They do, but it'd be bothersome to see your units running from the battlefield to the nearest supply depot.
-Why does Tychus take a sh*t in the Thor on that one mission when his suit has been attached to his body because of the debt he owes?
The CMC armors have excretion disposal systems for that kind of problems. It isn't hard to figure out that terran vehicles could have that same system implemented.
-Why is Nova so goddamn sexy?
Her polygons are sexy-shaped. Also, tight ghost suit, and since she's artificial, her creators could make whatever they wanted. Also, she has more in common with an Ultralisk model than with a real woman.
She's still sexy, through.
-If the Dark Templar have the ability to permanently cloak, why don't they share their technologies with the other Protoss units?
While terran Ghosts use a device to channel their PSI power to create a personal cloaking field, the Dark Templars are trained in the arts of manipulating the energies of the very void between worlds and stars itself, allowing them to constantly alter the light around them, creating the illusion that there's only air in their place. They don't share their "technology" to cloak for the same reason Jedi Knights don't share their technology to throw things through the air with just a hand movement.
-Why are battlecruisers the size of a few marines, yet if you zoom in, have thousands of little windows which are suppose to be rooms?
The commander (player) sees the battlefield and gives orders to the units through an advanced command and control interface where unit sizes are modified through virtual means to easy the commander's task of selecting the units to order.
-Why was Kerrigan neked when Raynor rescued her? Don't you think they would have brought some clothes?
"Jim: Hey, Tychus, we're going inside the greatest Zerg nest we've ever seen, putting all our chances on our faith in an alien artifact of a disappeared race that, in fact, we don't understand. I don't know you, but I'll leave some clips here and take some clothes in their place."
Also, when you're going to see if the most powerful psychic known for the moment (who can destroy a battlecruiser every 5-6 seconds, btw, and that in normal difficulty...), who is supposed to be the former queen and only leader of the currently greatest menace in the galaxy, is dead, transformed back into human or perfectly ready to destroy you all, and knowing that there're a few powerful forces interested in her, I'd not think much about if we're going to find her naked.
Also, Jim probably wanted to see her naked since he had no chance before her transformation. Chances are chances, dude. :3
-Why is Blizzard turning gay with their lore? I mean really, Hybrids?
Hybrids appear for the first time in a secret mission in SC1.
But creating just one campaign with 29 missions did much damage to the campaign's script. For the moment I prefer SC I to SC II (talking about story, script and campaign development). SC II: WoL is great in the last missions, Raynor's speech before the last mission was kinda moving, and the ending scene was great, but most of the campaign is pure filler.
-Why are there so many Chinese?
I'd ask where do they take the time to make more chinese children!

-Why is every picture of a unit the same, I mean can't they have like 10 variable pictures? Maybe some different voices to accompany?
All players look the same to units too. Also, Starcraft II already costed a lot of money to produce, it'd cost a 75% more to contract more voice actors, create more protraits and models, etc... Also, it already happens with the dark templars. Some games already have a random portrait, voice and model assignation for every unit, but it's too expensive to do so in a strategy game.
Also, clone vats.
-Why do all the BC captains have one eye, with one being metallic?
The great left-eye-eating parasite infection of 2474. It was a disgrace for the Koprulu sector population...
-Why don't nukes instantly obliterate everything in their AoE zone? Some buildings survive. I mean c'mon, it's a freakin nuke.
SC nukes are pretty small. Also, when you process some of the minerals native to the Koprulu sector (the minerals you gather in SC), you can produce some pretty hard materials.
-Why won't Kerrigan sleep with me?
The same reason you don't sleep with a steak.
-Why are all the THW smileys little orcs?
That has nothing to do with SC II logic, but... because it's a WC3 themed site?
-Why do the Zerg need observers to produce supply?
The Zerg don't need supply, their units eats the nutrients that the biomass extract from the very land. What Zerg need is psionic control. Overlords amplify Kerrigan's (or formerly the Overmind's and the Cerebrates'. Also, after Brood War, the cerebrate who the player incarnates is the only one who isn't killed by Kerrigan) psychic control over the minions in the planet and specially in the region. When all overlords are killed, the minions can still be controlled, but it takes the current lord/queen of the swarm more effort to do so.
-Why don't mother ships cloak themselves as well? Or at least have amazing hp, so they don't get auto-targeted? They cost a fortune anyway.
The Khalani protoss cloaking systems are based on extending a focused cloaking field under a ship, be it a Mothership or an Arbiter in SC I. Also, the radiation of the energy used to extend the cloaking field compensates and neutralizes any cloaking field extended over said ship.
ABout the Mothership HP, it isn't that hard to destroy anything whose vital points are as big as the Empire State building.
-Why hasn't the human federation sent more scout ships after the ones they originally sent never returned?
They did. The four ships they sent contained prisoners, and while the prisoners created their civilization, the original terrans of Sol developed as well. When the human federation transformed into the UED, they just sent an expeditionary force to try and take control of the Zerg, put the Dominion and the rest of the terran forces of the sector in their place, and then evaluating the protoss menace. Before that, the federation spied constantly the Koprulu sector, and it was, in fact, the existence of the Zerg and Protoss what united the human federation into the UED.
If the UED sent their entire fleet, things could have been different.
-Why didn't the last human federation scout send out a transmission before shooting himself in SC1? (I cant remember his name)
The Koprulu sector is 60,000 light years away from Earth. In 60,000 years someone might receive a letter from a dying general to his family.
-Why don't the Terrans just nuke Char from orbit?
They'd only kill the things on the surface. The true Hive is deep underground. The shockwaves of the nukes wouldn't do more to the tunnels than the tectonic instability of Char, and the climatic change is something you don't need to worry in that planet.
Also, if they destroyed char, the Zerg would have transformed another infested planet in their main Hive before the last bomb dropped. The original main Hive is the planet Zerus, and there are hundreds, maybe thousands, of highly infested planets out of the Koprulu sector.