The perk system in Fallout 4 definitely has room for improvement, as does the magazine system. Some minor recommendations for Bethesda if they decide to look in on this forum.
-A new magazine that series that adds back in the pyromancer, travel light, here and now, finesse, and hit the deck perks would make good magazine based perks.
-The cheme le femme/bachelor perk set (F3)
-The professional perk set (NV)
More to be added later, and by anyone else.