Thunderlord's Decree is balanced...
I will say this with full honesty. Currently many MANY champions benefit from the early damage output it does and the way it aids in the early game and laning phase. However, the sole reason it is the most common keystone mastery is because the rest is weak.
Wardlord's isn't great until you get your first crit item or two. Otherwise you need to sacrifice rune space for increased crit chance, and even then its a gamble. The healing is only done on champions. Is there a better mastery? Grasp of the undying. Much better, although it tends to lead to a more tankier mastery setting rather than offensive. Ergo, thunderlord's is better.
Fervor takes too long to proc early. It synergized nicely with AA reliant champions, but again really strives only later into the game, for champs like JAx or Yi. Early game, however, Jax benefits from the thunderlord proc for a stronger early powerspike in trades.
Deathfire Touch is my favorite on DoT champs like Swain and Malzahar. It counts, together with Corruptors potion, as a substitute for ignite, and does some hard extra damage. However, even it's damage output is only great after items and more towards the late game, though you want the early game advantage.
Stormraider's Surge is... useless. Bonus movement speed after dealing 30% hp. Great for chasing people down, but exhaust counters it hard, and you have to have burst. Talon used to use it well, until he benefitted more from the use of Thunderlord's when it got buffed.
Windseekers blessing is great. I see it used on any support who heals or intends to build with shields. It makes Soraka broken.
Grasp of the Undying is a good counter to thunderlords. It diminishes the early trade with guaranteed sustain, and allows you to win trades in lane by simply proccing the ability. I see it often on tanks in the toplane.
Strength of the Ages is.... Good, i guess, but it's not as useful as any other mastery. It stacks over time, but you want that early advantage.
This also goes for the final keystone mastery, Bond of Stone. Great on support tanks, but much more beneficial for the late game teamfights that most likely, if you appropriately abuse thunderlords, will never have to fight. Just generally, other abilities are better.
So why thunderlords? Thunderlord's decree provides powerspikes to many champions in the early. Vayne, for example, has a level 2 powerspike with the tumble W passive proccing even MORE early damage, increasing her late game threat. Same goes for Zed, for example, who has massive burst at level 3, which gets even stronger the more you level. Thunderlord's helps you win lane if you use it right. Grasp of the Undying is good for laning for a while and sustaining, but Thunderlord's gets you the offensive upperhard quickly, and guaranteed, in levels 1-6. If you use it right, you win lane... Plain and simple.
Hope this clarifies it for the people complaining about thunderlords. That mastery is not the issue. It's not too strong. the other masteries are just... weaker.
**EDIT**: OK Lemme clarify something about the masteries that seems to go unnoticed. You forget that there is another Tier of masteries you gotta pick out of. You could go 12-18 or 18-12, but figure out what you need. your choice. Magic Pen OR Armor Pen in ferocity, then a keystone, OR mapgic pen AND armor pen per level, or extra 5% CDR in cunning. IMO, getting both pens is nicer, because it's even more damage, but the CDR thing is quite strong too. 45% CDR is so strong. Then, Thunderlord's is the only offensive choice that is actually viable in lane.