Upgrade systems are a common way to offer a player an unfolding, shifting play experience. But often upgrades become conflated with the level-up system from roleplaying games - and in genres that do not require that system. If a player is presented with a skill tree that relies on simply raising numbers associated with their avatar, they may find that to be tedious if it doesn't make sense in the context of the game. This occurs often in first-person shooters that try to integrate leveling up - a game that relies on immediate player action conflicts with a system that abstracts those actions.
In Borderlands 2, the player's character levels up over time. Every level the player receives a skill point that they can spend in the skill tree. Some skills change the field of play in interesting ways - a player might add an AOE shield to their turret, or add a dash to their melee attack. But the majority are simple number buffs - faster health regen, better shield strength, or more ammo and faster reloading speed.
Furthermore, before reaching one of the interesting action-based upgrades, the player must pour five or ten points into these tedious number-buffs to qualify. It fills the valuable upgrades that offer a player new strategies or opportunities with boring, hardly-noticeable fluff, and as a result the whole system suffers.