I think it somewhat helps to pretend like you're holding the weight of the real world equivalent object that you're using in game as that's what the devs tried to go for, but like you said the pantomiming doesn't always translate so well.
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I think the thing they messed up on aside from general level design is forcing weapons being discarded at end of levels, like I get it they wanted to shoehorn in that ridiculous vending machine mechanic at the beginning of new areas but I suspect most players aren't taking the time to feed clip after clip of ammo just to get something they probably already used in an earlier area. Constantly stripping people of their arsenal and forcing them to rebuild it again each level is just annoying. Like maybe their thinking is they want you to improvise using the physics but I'm not sure if that really works most of the time outside of things like during the Streets level using trashcan lids for deflecting turret fire. Not really helpful against the moving enemies with guns.
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Thanks to a *lot* of your suggestions, I was able to sit down here before work and finish the Streets level in the game. It helped immensely to actually slow down my actions and make my movements more nuanced and 'weighty looking' rather than actually increasing my speed; I really wish the game could have explained it as well as you did.
Also, once I got a gun the moment-to-moment gameplay felt a lot better for me, since I think so far the gunplay stuff is shockingly well implemented; I really feel like I'm interacting with real weapons, and aiming down the sight (even closing an eye, just as I would at a range). I do wish there was feedback from the controllers, but overall it feels great.
Definitely seeing what you're talking about with taking weapons away. I started feeding ammo into the machine in the next area and wound up not getting the thing I wanted because I didn't have enough :\
Overall, I feel like I've finally found out how to deal with Boneworks. Even felt a lot more comfortable today moving around; didn't get any cold sweats or weird feelings despite a lot of silly things happening to my body in game. I really appreciate what Boneworks is doing, but I have to say, I'm looking forward to Alyx even more now (and my hype levels were already through the roof, since I got an Index for the game in the first place) since I think I am starting to prefer warping / room scale movement with non-IK interactions a bit more than Bonework's take. I bet they will complement each other well, though.