Glad you enjoy it!
I added some small quality of life changes for V1.4 based on your feedback: Increased size of 3225 crystal pads, changed USB C THT holes back to single oval shape, added THT pad under 32u4 to allow for the entire thing to be hand-soldered easier. Hopefully these changes should make the entire thing doable by hand. Unfortunately, without changing the crystal to a resonator and removing the 22pF crystals, it's gonna be hard to space out the components better, but it's good to know it's at least manageable!
By the way, if possible, could you post pictures of the completed boards? I'd like to update the github repository with the newest boards that people have done!
I wouldn't worry about the design that much. I think it's as good as it can be.
I'm not all that experienced with PCB design, but one potential improvement could be staggering the 0603 components a little. Don't align them in a straight line, but stagger them as much as you can. That would, I think, make it a bit harder to bridge components next to each other. On the v1.4 R1, R2 and R3 are done that way. R4 and R5 are not. C4 and C10 are, but IMHO not enough to be helpful. Because the capacitors are taller, and require a bit more solder than the resistors, they are easier to screw up than the resistors. It doesn't look like you actually have much space to play without though...nothing you can do about placement of C5 and C6, for example.
The size of the pads on the crystal don't matter that much if the crystal itself only has bottom pads. Those are always a problem if you're hand soldering.
The 32u4 is also fine. I know you can't use the 32u4-AU, because there simply isn't enough space for the legs on the board. The AU model would be easier to solder, but the soldering on the MU isn't that much harder. It is harder to spot the bridges though, especially if your eyes aren't what they used to be (old age doesn't come alone...).
Anyway, all this stuff is moot, if you use a hot air gun. I should receive the one I ordered later this week. Definitely going to use it to assemble a few more Alvaros. It should go much easier than hand soldering.
I'll take some photos after I do that. I'm curious myself to see the difference in the hand soldered and hot air gun assembled boards.