1. Trademark trash collecting as an underlying mechanic that takes a lot of gameplay. I still can't imagine why someone sees picking up banana skins as something I'd like to be doing in a computer game, but there you go.
Kinda. It's not that big of a deal, and you end up carrying a bunch of stupid +1 HP soda cans and other crap in SS2 as well, but they really could just skip the trash and have recycling/crafting mostly be used to convert some resources into others.
2. You can be sure that point one will be connected to a crafting mechanic that, while robust, is ultimately pointless, since you don't really need it and it's not fun. Like someone pointed out, why the hell is crafting weapons even an option when they don't degrade? On the other hand, the few items that are in fact useful completely break the game. Neuromods, lol.
On Nightmare I certainly needed to craft a bunch of ammo, I imagine you'd need even more if you wanted to use the more exotic guns. As someone who uses two pistol clips on a Phantom, you should be able to understand this. And you can craft weapons for the sake of flexibility - you can decide that you don't want a particular weapon to take up inventory space (Q-Beam in the early game, for instance), so you recycle it, and then you have the option of crafting it again later on if you want to. Don't see why this is so difficult to understand.
Making Neuromods is definitely dumb though. Maybe it wouldn't be if exotic matter was much difficult to come by and you needed to actively hunt more Typhon for it, but as is, there's little reason not to mass produce mods in the mid-game.
3. The difficulty not coming from any interesting mechanics, but the fact that higher difficulty levels result in some enemies dishing out ridiculous damage, while at the same time taking even more ridiculous amounts of ammo to kill. On hard a phantom can kill me in two shots, while the first shot leaves me with like 20-30 hp at full armor. At the same time it takes like two pistol mags to take down. The first time I've met Technopath I've used all my shotgun ammo to kill it, while shooting at point blank range. Fun combat indeed.
Meanwhile, the difficulty in SS2 came from all the interesting combat mechanics and enemy behaviour? Enemies are quite tanky indeed, but that's balanced against the relative rarity of the tough ones. There's never any more than one Technopath or Telepath in a given level, and Phantoms are similarly rare at the beginning of the game, when they actually require significant resources to kill.
Besides, you're either exaggerating or don't understand the damage mechanics. Disabled enemies take more damage (what disables them depends on enemy type), and all enemies also have weak points. I guarantee that if you EMP a Technopath and shoot it in the face from point blank, it'll go down relatively quickly (unless it's an unupgraded shotgun and you have no Security weapon talents, in which case maybe Fallout 4 is indeed the game for you). A Phantom also never takes two pistol clips to kill, not even with an unupgraded pistol and no buffs.
That's not to mention that there's almost always some way to use the environment to do tons of damage to enemies. Technopaths specifically, for instance, have no way of breaking out of GLOO, and take massive fall damage once completely frozen. I literally killed the first one I met by accident this way.