About the burnt shadows topic, I also think you still have almost black shadows, while it seems realistic to me under a vivid sunlight, I'm not fond of this part of our reality 

I tried to find some light and dark balance that would please me without going too far into the black, I used your first and last attempt at trees:



Now for the eyes killing grass, I don't know, its also related to how big the screen size is (if it is a game), the smaller the screen, the less attention this grass will draw in terms of mass. How about a sneak peek at Minish Cap, approximately twice screens:

I can't quite judge what's happening to the pixel cohesion and neighboring.

I totally concur on your issue with 1x. As far as I trust what my eyes are actually seeing, 1x usually not do justice to what I'm trying to pixel. But obviously, putting aside "matters of taste" (if possible), as Helm and Ptoing already highlighted, something may be wrong. Personally, I begin to understand that an awful CRT bias might goes on as I'm probably placed in minority by non-CRT viewers, but given your screen specs I doubt you're viewing pixels with cathodic tubes.

I made http://www.pixeljoint.com/pixelart/79725.htm using 2x preview, and always thought it looked better 2x.

Well I do prefer your piece at 1x, actually, at 2x I think some places are a bit crude, lacks AA like clouds, color gradient illusion not working in mountains, ordered dithering in rocks, jaggies on pine trees. Whereas at 1x, none of these small "flaws" apply in my opinion.
At 1x the illusions works perfectly to me.

I'm also blocking scripts but it isn't an issue for me, temporarily allowing the zoom script is just two clicks away when I fire up my browser. As for the resolution 1280*1024 96dpi 19'', and I rarely look at (or even push) pixels at 100% zoom, it just "doesn't feel right" to me anymore, so I end up click zooming to view everything at 200%.

Having the ability to zoom in also does greater justice to pixel pieces that use dark values, it bypasses the cons of the bright SMF default skin.

Legend of Iya made it. Thought for sure funding was going to fall short - I checked 2 days before deadline and there was s huge defecit still. Surprising . . .

A great victory for the metroidvania genre ! 
...I'm still a bit concerned by the game's acronym though

I remember reading an interview with a former pixel artist in the gaming industry where he briefly described his process, pixel pushing with a joystick: "clac, clac, clac, tic, clac, clac, tic, clac, clac, clac"

This is so alien..
I can't even imagine doing some pixelling without 32bits tools like curve control, smart saturation adjustments, layers, infinite RAM, and so on. That being said, I think Deluxe Paint (II? or maybe the III) was kind of a revolution for hard working artists back then.