A fine essay.
Where I agree: The introduction of Sean Connery's character is a masterstroke, and I agree entirely that this is the Indiana Jones film with the most emotional heft, containing a far more moving "Let it go" than a certain Disney film (ironically involving another Elsa who couldn't let it go).
The action set pieces are good (especially the tank chase), and the invisible bridge sequence is a stand-out (and a dramatic high point), but whilst it comes close, I don't think this one tops Raiders.
Which is where I disagree: I think Raiders has 1) the superior set pieces (opening tomb raid, fight in the Nepalese bar, the Cairo chase with the Arab swordsman, the map room, the snake pit, the fight by the plane, the truck chase, the absolutely brilliant (and terrifying) Old Testament finale, the enigmatic final scene, etc), and 2) the subplots you claim don't exist. For instance, the relationship with Marion, rekindling their romantic spark (albeit this time less dubiously, given the hints about Indy taking advantage of her as a teenager), and also in relation to Belloq. The scene where Belloq says he is a "shadowy reflection" of him is key, as Indy is a darker character in Raiders; essentially a grave-robber who is just as obsessed with finding the Ark as Belloq and twice abandons Marion as a result of this obsession. Only with his realisation in the finale that a seriously scary Old Testament God isn't about the let Hitler and the Nazis co-opt his power does he realise he needs to let Belloq run with his obsessive folly and to simply stand out of the way, whilst "not looking", akin to the story of Sodom and Gomorrah when Lot's wife is turned to a pillar of salt for looking back at the destruction. It's also akin to the story of Shadrach, Meshach, and Abednego, who were cast into the fiery furnace by Nebuchadnezzar, but did not burn, and only their ropes were burned away (as Indy and Marion discover, after the fact). Perhaps it's because I'm Jewish, but I always thought the Ark of the Covenant was a far better MacGuffin than the Holy Grail (although the Grail works too, as a metaphor for the fact that the true "Holy Grail" is Henry's restored relationship with his father).
So, in short: Indiana Jones and the Last Crusade is a terrific film - one of my favourites - and it certainly comes close to matching Raiders of the Lost Ark. But it doesn't quite, in my not particularly humble opinion.
More of my thoughts on Last Crusade here, if you're interested. :)
Indiana Jones and the Last Crusade: Where It Should Have Ended? | Fanfare