The perks and their weaknesses exist to drive the plot, which is, y'know, normal.
In-Universe
As of this chapter, the game just launched (probably with a restrictive beta period) and literally all theorycrafting done about the game is likely made with secondhand knowledge and the patented internet standard of Jumping to Conclusions. Plus Earth doesn't strike me as the kind that would do extensive research before jumping in.
Aka Earth decides on the value of perks based on youtube comments and capslock forum titles, which is likely not the most accurate of sources.
To break it down with possible reasons (as if this was a real game):
Archery - if aiming isn't computer assisted, then melee is just more accurate.
Stealth - again, if aiming isn't computer assisted, then melee is better. Plus, given it's an MMO, anything bigger than a mob unit will have bundles of health. Why spend two perks (Stealth+Archer) when you can take a melee skill and something else that's consistently good?
Potions - Take something that complements your melee so you don't get hit.
Phys boost - Again, take something that complements your melee so you can get your kills in faster.
Kick - see above.