Most the OP's complaints fall into 2 categories:
1) Not understanding 5E rules.
2) Liking Baldur's Gate 1 & 2's ruleset more.
You're fine to have your opinion, OP, but a post like this is akin to having your friend bake you his first professional cake after he graduates culinary school. He gives you a slice and asks your opinion, and you say 'It's not pie. I like pie. I like the apple pie I had last year. Why can't this be more like that pie?'
It's information, but nothing your friend can use in regards to that 5th Edition cake he made.
For your information:
Weapon proficiency is weapon proficiency; if you are proficient with a weapon, you add your proficiency bonus. If your Prof Bonus is a +3 and your proficient with Short swords; add +3 to your attack. And add your Str mod to the damage. It does not matter if you're a rogue, a warrior or even a mage. If you are proficient, you can use that weapon to it's fullest effect.
And spells have been able to miss since at least 3.5; a ranged touch attack spell misses if you don't hit the characters flat-footed AC. A ray attack can be dodged.
I think only area of effect spells can't miss, but they can be resisted.
And weapons have a flat damage. It's not Larian's choice if weapon <x> has a higher damage than weapon <y>. It has nothing to do with Larian balancing the weapons or 'not grasping' any importance.
And I believe your Proficiency Bonus is also added to skills you are Proficient in. IE: Anyone can do any skill, but you won't get that sweet +3 Prof. Bonus added on unless you are Proficient in it.
And your Background gives you 2 Skill Proficiencies. Not weapon or armor proficiencies.
I don't think you even get skill points anymore. It's just your Ability Mod + Proficiency (If you are proficient)
So, again; many of your complaints boil down to either not understanding a new ruleset (which happens to everyone) or just liking AD&D more.
All you have said is correct, that is the way 5e handles proficiency.
