Encumbrance -- I agree with the OP, too much hassle. We use an informal system that lets you carry "four hands" worth of weapons (a polearm and two daggers, or a bow and a greatsword, and so on). As for potions & scrolls, a dozen of each. Other stuff? We don't sweat it.
Material Components -- Really, what do they add to the enjoyment of the game? it's a hidden tax on spellcasters! I just assume the caster has what they need on their person. The only exception is when a material component has a listed cost -- I do require the player to pay the cost, but I don't make getting the materials part of roleplay.
Multiclassing XP Penalties -- I never enforce it. But if a player wants their PC to multiclass, it has to make sense in-game. A bard can't take a level as a rogue for example, unless she knows a rogue PC or NPC who's willing to train her between adventures. Adding a new class when you level up during an adventure is a usually a no-no.
However...
If I were forced to play with a group of metagaming min/maxers instead of the immersive storytelling/all-in-good-fun group I enjoy now, I might have to start playing it by the book.