OP does not understand how real guns work or how game balance design works, at least based on the OP claims.
The various complaints you have made are intended and accurate design for either real life or game balance. They are what they should be, at least as far as your examples.
For example, a Minigun is a short range weapon just like a shotgun. It fires small, low damage projectiles but does so at a very rapid rate so that many small projectiles hit targets as long as the targets are fairly close. If you fire a Minigun at anything a fair distance away, most projectiles will miss.
The same thing applies to full automatic weapons such as submachine guns or assault rifles. In fact, the actual complain that should be made for these types of weapons is that the AI is FAR too accurate with them even at medium to long range. Automatic weapons are very inaccurate by nature, just like a Minigun, but they are not intended to be accurate. Instead, they are intended to fire many rounds at a very fast pace so that it is more difficult to miss with some rounds.
Basically, these types of weapons use the concept of percentage victory rather than the sniper, sharpshooter mindset of "one shot, one kill". They are intended to hit several times, miss with the majority of their rounds, but the several hits will add up to good damage at a rapid rate. They are also useful as distractions / cover fire, unlike sniping, single shot weapons. This is basic weapon design.
As far as creatures are concerned, the higher level creatures do not necessarily need to have higher health. Higher level =/= higher health, ever. You have many creatures in real life that are very weak physically and easily killed but are extremely dangerous due to elements such as poison or other abilities. For a game, this real life element is useful for game balance, just like with various weapons. A glowing deathclaw would not have higher health because it never needs to evolve that way since its radiation kills most things faster and it won't have as many protracted fights. That's just one example from the OP list, but everything follows this type of evolution (and game balance).
It is possible that there may be some mistakes in the .ESM, of course. I found four weapon mistakes/typos in Skyrim, for example (i.e., weapons that had incorrect stats based on comparing them with other weapons of the same type and material, such as an Orcish Dagger having an incorrect range compared to an Iron Dagger even though all other Daggers have the same range). However, that is out of all the weapons in the game, even unique ones, so that is a very small number of legitimate errors/oversights.