At the end of the day, I honestly don't have a problem with what Alpha Legion has been shown to do. I don't think it comes down to an outright statement of unreasonable superiority on the part of the writers. The Legiones Astartes, for the most part, are a force that focuses on shock assault. They are an overt force that demolishes and annihilates whatever is put in front of them.
There are a few exceptions, to be sure. The Night Lords, for instance, are more likely to focus on terror operations, psychological warfare, and tactics that allow a collection of selfish, vicious criminals survive. The Raven Guard certainly employ stealth and heavily rely covert infiltration for their operations.
The Alpha Legion aren't so much better than the other Legions than that they simply chose to play a different game altogether. They succeed against their brother Legions not because they are necessarily stronger, faster, smarter, or whatever. They simply employ different tactics - ones that the other Legiones Astartes find distasteful and - this is important - unnecessary given all the firepower they can bring to bear.
Put it this way. Most Space Marines are a seven-foot-tall mix of Bruce Lee, Arnold Schwarzenegger, Usain Bolt, and Audie Murphy. If, one day, one of them opens the bulkhead to their quarters and gets sucked into the vacuum of space, does that mean the Alpha Legion are better warriors? Or does it simply indicate that they didn't expect someone they considered their ally to sneak aboard their battle-barge and cut a hole in the hull?
And once he does realize that the Alpha Legion are enemies, does the Space Marine's inability to counter their machinations indicate he is inferior in terms of martial prowess or intelligence to them? Or does it simply indicate that the Alpha Legion are far more experienced at this sort of thing, that the Space Marine is reacting (always a bad thing), and that there are a lot of things (like, a galaxy-wide war) distracting him from anticipating all sorts of devious espionage and sabotage?