The sense of mystery and dread that you mentioned touches on the only part of the article I disagreed with - the critique of the "pointless" weapons, of the game giving you a sub-par base and sub-par craft to begin with, and basically no guidance is what made it such an adventure.
X-Com (the organisation) truly feels like a hastily slapped together ragtag bunch in the beginning. Governments have thrown money at a problem with no real plan or strategy and whipped up something ASAP. They want results and it's your job to deliver them. You're the expert, they're more than happy to pull out if you fail. You are probably unprepared, but no one had any idea how unprepared, something you very quickly learn after your first encounter. That elite squad you outfitted with all of mankind's best aircraft, armour and weapons? Just got owned in their first encounter. Medkits? Basically useless when you're being melted by a single plasma rifle charge.
The clutter and disarray really drives home just how vastly outgunned humans are in the beginning and the story driven by player experience would suffer greatly if all the "useless" stuff was pared back and the starting condition pre-optimised.
Otherwise a great article.