I see these arguments against Starcraft 2 a lot, and I mean this with the utmost respect, but it's fairly obvious you don't quite understand the decisions Blizzard made with Starcraft 2. Blizzard wasn't totally oblivious to the last 12 years of RTS/RTT development, they deliberately chose to ignore the developments, which sounds like a bad thing but they had good reasoning behind these decisions.
Why aren't there automated gathering structures?
Simple answer: there's something to harrass. You cannot harrass a building - workers are very fragile in SC2 for a good reason, so players can use fast units to get in, do some economic damage, and then get out. Destroying a building is a lot harder than killing the people working for it. It therefore encourages players to defend their mineral line from attack, as well as opening up more strategies for the opposing player - do they try and out-macro their opponent and win in a straight battle, or do they strike at the economy and weaken them enough so their army can them finish them off?
Why must I construct additional pylons?
This is to raise the skill ceiling - you said it yourself:
At its heart, Starcraft is an economic game first and a tactical strategy game second.
Starcraft is a strategy game, so constructing additional pylons to be able to accomodate all your units is part of the strategy (it also prevents players from amassing huge armies too quickly). Same goes for building additional production facilities to be able to spend all the money you're acquiring. This is why you lose money instantly for queuing up a unit because you need to only queue up one at once, this is why there's no option to automate the unit queues. The AI is bad in this game, but it's bad so you have to keep on top of your units.
But of course, you addressed this:
The problem with excessive micromanagement is not the that it doesn't require skill, but that it adds nothing to the game
[sub]By the way, it's macromanagement, not micromanagement. Micromanagement = controlling units, Macromanagement = managing your base, resources etc. Anyway:[/sub]
It most definitely adds something to the game, and it is not 'random', it is part of the strategy. It's annoying, but it's there for a reason - it makes the game harder to master, as well as making it easier to separate good players from bad ones. Starcraft 2 is designed to be a competitive game, and to make a good competitive scene, it needs to have a high skill ceiling. If someone can play the game for only 300 hours of so and be a master of it, then why bother playing 10,000 hours of the game when you could play 10% of that and just do as well? This is why CounterStike is bigger competitively than Call of Duty, and why people play Street Fighter 4 at tournaments and not Super Smash Bros. Yes, competitive scenes for those game do exist, but they are a lot smaller. Removing all this macromanagement will make the game more fun for a casual player, but it won't encourage people to play your game for as long as the original Starcraft did. And since hardcore players are essentially your most loyal customers, you can hardly be surprised that Blizzard didn't 'dumb down' Starcraft 2.
Why do I have to sit here and build workers for several minutes before anything happens?
The downtime at the beginning of the game is also there for a reason, to give more options to the player which strategy to go - do they cut worker production to go for an early rush (e.g. 6pool, Cannon Rush) or fast expansion? Or do they play standard? This leads to more variety in strategies - more variety = more fun to play competitively, as it prevents the game from getting stale.
Why can that tank hit a unit up a cliff when it's underneath it?
This one's easy - Starcraft's designed to have simplistic combat. It focuses on macromanagement, not micromanagement; yes micro is very imporant and one bad engagement can cost you the game, but macro is way more important. It's dumb, but no one said games had to be realistic (and if they did they are wrong).
Why must there be all this research? Why don't High Templar spawn with Psi Storm enabled? etc.
Balance. Recently the Protoss Warp Gate research time was increased by 20 seconds. Why? Because Protoss v Protoss matchups were becoming dominated by one strategy - the 4Gate, which made the matchup boring to play. By delaying how long it takes before the Protoss can get Warp Gate, it allows other strategies to come into play, since they no longer take longer to deploy. Now Protoss players can continue to go 4Gate, or they might use Stargates, Robotics facilities, fast expand etc. because now they get execute their strategy and have time to prepare a counter for the 4Gate push.
This is why High Templar don't spawn with Psi Storm enabled. Because otherwise players could get out Psi Storms way too quickly, and that would mess with the balance - you could ask why didn't they just increase the build time for the Templar Archives, but then that would have a knock-on effect on balance as well, the player can build a Templar Archives now and warp in High Templar whilst researching Psi Storm, so when the research is complete, he has HTs ready to storm, as they have got enough energy. Otherwise he'd have to wait just as long to get out HTs, but they don't have enough energy and are mostly useless for a while.
Also:
The attack and defense buffs are utterly pointless
No offense intended, but you could not be more wrong. They are
very important. Ask any high-level player.
Why didn't Blizzard innovate?
Because they didn't want to. You don't have to innovate to make a great game, and innovation for its own sake instead of innovation for a good reason is silly. No more than that, really.
Final thoughts
I just want to point out that not liking RTS games that focus more on Macromanagement is merely preference so there's no point me arguing against you for that, but equally, it's not bad design like you said. Also, as other people have said, that is a very long post (I did read it, however) so you'll need to trim it down in the future. A lot of things were mentioned twice, first in the 'what is wrong' and then 'what should be improved' section.
[sub]However, looking at my own post, I can hardly talk.[/sub]