Well...
It seems to me that you didn't read my link.
I explained there, firstly, that the Ma5 series DOES have iron sights, it's under the electronics's suite which is removable, as seen in this image:
And the elctronics suite is more than just a compass and ammo meter: It provides other functions too (admittedly, what these are isn't really said in detail)
As I explained in that thread too, it's mentioned in canon by many individuals that the MA5's are deceptively sturdy, and that we almost never hear about Ma5's breaking or jamming in canon unless they get outright destroyed (and it's not like guns never break or jam in the Halo novels).
You have to remember that this is 500 years in the future: What we can now fit in a flash drive would have almost the same amount of memory as a full sized computer of 10 years ago.
In 500 years, there would almost certainly be lighter but stronger materials to make guns with, electronics will take up minuscule space with greater memory, And guns have only really been around for 500 years (unless you count a tube with a bunch of powder stuck in it a gun), what will 500 more bring? There are so many improvments that may be in the Ma5 that wouldn't be apparent if every weapon has them.
As for the other things you said (nearly all of which is addressed in that link, BTW):
The M6d's scope is right above the barrel, it's the thing that looks like a laser sight emitter:
The way it works is that it is uplinked to the users HUD, be they a spartan in Mjonlr armor, a ODST with their helmet, or a Marine with the eyepieces. The reticule ins't just in game: it's a canonical thing, too, that's why the MA5's have their iron sights covered by default, most soldiers have a HUD.
As for the shotty, this is outright stated in canon to be due to advancements over the 500 year course, in fact, the recoil is stated to be "relatively low" by a marine.
The guy who designed most of the UNSC gear, rob mclee's, actually considers a lot of this stuff when he designed them, and calculated the muzzle velcoity these would have, how they would behave, how fast the vehicles would go, etc.
About the warthog, the model you see in game is just one vairent out of many. Yes, it is rather open, with no door and such, but I don't think you realize how large the vehicle is.
For normal, non spartan passengers, the walls are so big that doors simply aren't needed.
The covenant's weapondry may not seem all that practical or powerful in game, but that is merely for gameplay purposes.
In canon, a single shot from any plasma weapon is often deadly. (you ARE getting shot at by what is essentially a small orb of lightining)
To answer your question, the covenant are shown to actually be pretty bad at reverse engineering forerunner stuff. What they use is only a fraction of the weapons what the forerunners had, and many times weaker.
