Basically the way it works out is that the "LEFT" side is the offensive option and the "RIGHT" side is the defensive option in a pair.
Firstly lets go on about Protoss Research
Ultra Capacitors - Your Attack upgrades now increase your unit's attack speed by 5% per upgrade
Vanadium Plating - Your Armor Upgrades now increase your unit's Hp by 5% per upgrade.
Now, this depends on your playstyle really, if you are ultra aggresive, I.E YOU WANT TO RUSH AND NOT TURTLE SO MUCH, then it actually turns out the life upgrade is better, it means you can move out that much faster.
If you want to turtle in your campaign, use bunkers, siege tanks etc to defend then the attack speed upgrade is better, because they mean you fire more often before the enemy hits you, and because you are in bunkers or your tanks are in entrenched positions, their hp doesn't matter so much.
This upgrade is entirely up to the individual player, I personally prefer the attack speed upgrade, I would recommend it if you like Siege tanks in anyway shape or form :D.
Orbital Depots - Supply Depots now Drop in "Instantly"
Micro-Filtering - Your Refineries now harvest gas 25% faster.
This research is more dependent on how "good" you are, if you are bad, like me, Orbital depots is BY FAR the best option, it means you don't have to constantly produce depots and can just produce 2-3 at a time by 1 scv every so often and not be supply blocked.
If though you are good at managing your supply, then Micro-filtering is better, but to be honest I have gone through all missions and there was no mission I really thought I needed my gas 25% faster, considering medic marine is like such a powerful strategy, you just don't need this upgrade unless you have no use for Orbital Depots because you are awesome :D.
Automated Refinery - Your Refineries now harvest Vespene Gas Automatically
Command Centre Reactor - Your Command Centres can now Produce 2 Scvs simultaneously.
Ok, this choice is pretty simple to me: AUTOMATED REFINERY, every time. Although the reactor is useful, the point is that on alot of missions you can't produce 2 scvs at a time at the start anyway because you don't have the mineral income to support it. Also the Automated Refinery means you usually get a few free scvs per mission because they were given to you to go on gas ideally at the start, but now you can put them on minerals instead.
There is also one mission, Supernova, that having the automated Refinery is just SO USEFUL. In my opinion this upgrade is mandatory.
Raven - Drops PDD, Turret and can use Hunter Seeker Missiles, Detector
Science Vessel - Can use Irradiate, Repairs Vehicles!!!!!!!!!!!!!!, Detector.
Now although you can't get science vessels in multiplayer, my god I wish you could, they are amazing, there is no choice here you HAVE to get vessels here in my opinion, the raven is just not worth the money in single player, it requires too much micro to be good, but to have a free heal on your mechanical units (IT DOESNT COST EXTRA MINERALS/GAS :D) from science vessels makes this upgrade pretty mandatory imo. Once you get vessels you will be making them, pretty much asap.
If you want to practice "TERRAN PLAYSTYLE" for multiplayer then get a raven sure, but science vessels are like 9000% better :D.
Tech Reactor - Combines the Tech Lab and the Reactor
Orbital Strike - Units from your barracks now arrive in drop-in pods at your barracks' rally point.
Now, this depends on your style, if you are protoss, or like their style over terrans. Orbital strike basically converts barracks into Warpgates, although you still queue, you get to reinforce anywhere, you can basically drop in a force anywhere on the map, which can be awesome for certain missions, Shatter the sky for one. It's also awesome if you basically only want to go medic/marine since you just need reactored barracks for that strategy (later on).
However, I personally prefer lots of siege tanks, banshees, medics and marines. So I would go for the tech reactor as it allows multiple siege tank and banshee production. It also means I don't have to buy the medic upgrade of course. This is really down to personal taste, neither of these are mandatory.
Right. ONTO THE ZERG UPGRADES.
Shrike Turret - Adds a turret to your bunkers that attacks ground and air.
Fortified Bunker - Adds 150 life to your bunkers.
There isn't much in this really, It really depends how you use your bunkers, if you use them primarily for defense, alone, then you are probably better with the Shrike Turret. If you use them, like I do, as like a stopper for your Siege Tanks to obliterate your enemy when defending then the Fortified Bunker is a better upgrade.
Really though, the differences here are minor, just go with what you feel like :D.
Planetary Fortress - Allows your Command Centre to be outfitted with a cannon at the expense of being able to lift
Perdition Turret - Flame Turret
This is again optional, HOWEVER, I will say that the final mission is MUCH MUCH MUCH MUCH MUCH easier by going with the Planetary Fortress option, The Perdition turret is just really weak in the final mission compared to the fortress. The Perdition Turret has more uses in like other missions than the fortress does though, since mostly you can't expand on most maps in the campaign, where the fortress shines in multiplayer.
However I would personally go for PLANETARY FORTRESS, just because it makes the last mission so much easier.
Predator - Anti-Infantry Cat like Vehicle
Hercules Transport - Massive Transport that unloads units almost instantly
The difference between these 2 are minor, Hercules takes alot of tech to use and isn't that useful in most missions, however I would say it was better than the Predator because it means you can ignore medivacs in the campaign.
The predator is only really useful in like one mission (welcome to the jungle) otherwise it just isn't that great, you really won't make them once you can make siege tanks.
But again, it doesn't matter: neither play a pivotal part in the campaign, just go with how you feel.
Cellular Reactor - All units start with +100 Energy and +100 Maximum Energy
Regenerative Bio-Steel - All Mechanical units slowly regen life.
Basically: TAKE CELLULAR REACTOR, if you followed my advice and took the science vessel.
Regenerative Bio-Steel is kinda useless if you have a science vessel able to heal your units with your mech units. Cellular Reactor means all your energy units have 125 energy+ out of the gate, which is just immense and means they can use their abilities right at the start, it's particularly useful on the mission "Supernova" and on other missions aswell.
Hive Mind Emulator - Allows you to mind control zerg units in a SMALLLLLLLL!!!! radius around the target.
Psi Disruptor - Slows nearby zerg AND THEIR ATTACK SPEED by 50%.
Do not be conned by the hive mind emulator into thinking that it is cool, although you might want a pet ultralisk, on most missions they die too fast or don't go in range of your stinking emulator for you to be able to use it. Basically the Psi Disruptor is SOOOOOOOOOOOOO good, it means that the zerg units are 50% slower so your siege tanks have twice as long to kill them before they reach your lines, (Or even your bunkers).
So yeh take the Psi Disruptor, it is SOOOOOO useful, on sooo many missions (wherever you will be attacked by zerg) the hive emulator is too gimmicky to be of any real use D:.
a TLDR of Sorts will be listed here:
Protoss: Ultra Capacitors, Orbital Depots, Automated Refinery, Science Vessels, Tech Reactor
Zerg: Fortified Bunker, Planetary Fortress, Hercules Transport, Cellular Reactor, Psi-Disruptor.