Sorry, can't relate to any of the points in OP. Iron Sights are supposed to be harder to use than especially the reflex sight, and I love the way this is modeled. I haven't noticed, but maybe barrel length has an effect as well wrt "weapon inertia"? It's supposed to be an upgrade (not restricted to VATS only players) rather than just visuals. Can't remember if the reflex sights are "accurate to the real world" because the fights have been too hectic for me to notice, but I did enjoy the fact that the "reticle" was in fact moving in the sight indicating this would be the case (rather than just a texture painted dot in a glass, which many games do/did).
Some ammo is rare, deal with it and just buy the stuff, pick appropriate perks to reduce the ammo wasting factor, and use chems and clothing to boost what you need. This is supposedly a CRPG where the challenges you face change depending on what choices you make during character buildup. The same goes for different weapon and armor mod configurations, there isn't a fix'ed "best way", but a way the best matches your chosen playstyle. Not having all options available for all guns? Seriously? I've never done a tabletop RPG that allowed this kind of nonsense anyway. Use game mods to "fix" your game to your liking, don't "fix what ain't broken".
About difficulty being bullet sponges. Well, yes and no. The game is kind of lacking in the role playing mechanics, but still a great first person shooter and exploration game. The purpose seems to be "the road you choose to becoming godlike", and can vary pretty good depending on starting parameters. Playing on higher difficulties means you have to utilize more of the games options in order to succeed with tougher enemies - exactly what was expected of us in tabletop RPG times by the GM, and he would even reward us with additional XP if we successfully utilized available mechanics to achieve a successful outcome, while in FO4 this reward system is a bit shallow. Failure to use such mechanics (chems, proper weapon and armor mods, foods to boost HP etc) while still complaining about bullet sponge effect doesn't make sense to me at all. Sure, other ways of handling it would be possible in tabletop games (more enemies, or adjusted specifically to the situation and party facing them), but not very valid for a CRPG (for coding complexity reasons). and I have a hard time imagining what could be better within "the same system" (better AI behavior does not fall into this realm, nor does "dynamic AI perk tree evaluation" like a living GM would do).
They've tried to satisfy realism fans and casual players - this is obviously kind of a conflict zone. Gameplay for a "realistic shooter" would be horrible wrt CRPG. Although I wouldn't mind more realism. However, hard to use iron sights are for me very realistic, and acts as a mechanic for me to want to upgrade them.