Meaningful Masteries
Problems in power for masteries have always amassed great inbalances and annoyances. What I blame for this mastery problem is the sheer number of masteries one can have in any given game. This large number makes it incredibly easy to make masteries too weak or too strong. Either the masteries give a number of insignificant buffs that don't actually make any difference in game-play or the masteries give a number of strong buffs that start monoplizing the game.
My suggestion is simple: pick one mastery from a number of others, much like a summoner spell. Have some 15 or so masteries to choose from where you only pick one. They would reside within 4 catagories: aggressive, passive, strategic, and skillful game-play.
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Aggressive -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Instigator: Instigator causes you to deal +7.5% damage to champions.
Brute Force: Brute Force causes your crowd control to last 7.5% longer on champions.
Ferocious: Ferocious causes you to deal +1% damage to champions for every 8% health you're missing.
Fresh Blood: Fresh Blood causes your next basic attack on a champion to deal 45 (+2.5 per level) (+22.5% attack damage) (+12.5% ability power) mixed damage, (+50% if you are melee). This has a 14.5 (-.5 per level) second cooldown.
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=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Passive -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Pacifist: Pacifist causes you to take -7.5% damage from champions.
Slippery Touch: Slippery Touch causes crowd control done to you from champions to last 7.5% shorter.
Perseverance: Perseverance causes you to take -1% damage from champions for every 8% health you're missing.
Wind Speaker's Blessing: Wind Speaker's Blessing causes your shields, heals, and movement speed boosts to be 15% stronger.
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-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Strategic -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Fire Bombs: Fire Bombs allows you to place a bomb on the ground 100 units in radius. If an enemy champion runs over this bomb, 90 (+5 per level) (+45% attack damage) (+25% ability power) mixed damage is dealt in a 400 unit radius. These bombs are visible but untargetable. The cast range is 1000 units and they take 1 second to arm. This has a 48 (-1 per level) second cooldown and a 3 charge limit. You can have up to 9 on the map at a time and they do not short out. This mastery is assigned to hotkey T.
Shade Caller: Shade Caller is a 2 cast mastery. First cast: a shade stands in the position you were when you cast it and is seen by all players. Second cast: after a 4 second channel, you teleport back to your previous position. Unless the enemy has sight of your champion, they cannot see you channel, but when you finish, the shade will disappear. This has a 120 second cooldown and is activated with the hotkey T.
Hextech Design: Hextech Design allows you to select one summoner spell to give a 2 charge limit to (4 for smite) for the rest of the game. If you want to reassign this mastery, it has a 300 second cooldown and is assigned to hotkey T.
Spectral Sentinels: Spectral Sentinels allows you to target 3 spots anywhere on the map to assign a sentinel to. These sentinels stay until replaced and provide 400 units of sight as well as +20% movement speed to allies in range. Enemies who have vision of these sentinels can see them standing guard. They do not reveal invisible or camouflaged units. They cannot be destroyed or hindered by ward disablers or things of similar manner. If you wish to place or replace a sentinel, it has a 300 second cooldown and a 3 charge limit. This mastery is assigned to hotkey T.
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=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Skillful -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Poisoned Impailer: Poisoned Impailer releases a skill shot that marks and stops at the first enemy champion hit. This mark makes that enemy take +5% and deal -5% damage for 2.5 seconds. This has a 30 second cooldown and a 3 charge limit. A single enemy can have multiple marks on them at a time and each one will take effect. This goes up to 500 units and is assigned to hotkey T.
Spectral Talent: Spectral Talent turns you untargetable for .75 seconds. During this time, toggles turn off and no abilities or basic attacks can be cast. This does not interrupt movement. This has a 30 second cooldown and is assigned to hotkey T.
Healthy Heartbeat: Healthy Heartbeat causes an indicator in a rectangle to go back and forth while in combat with an enemy champion (takes about .75 seconds to get from one end to the next). If you press T when it enters the very center, (about .25 second sweet spot), you regenerate 3% of your maximum health over the course of 3 seconds. It has a 3 second cooldown (regeneration occurs during cooldown) before you can reactivate this mastery to try to hit the center.
Lunge of Faith: Lunge of Faith causes you to lunge 250 units in a target direction. If you pass through an enemy champion, its cooldown becomes 1 second, if not, it has a 30 second cooldown. This cannot pass through terrain and is assigned to hotkey T.