Regardless of everything you just said, the choice for each champion is relatively obvious. You don't need a thousand mastery pages to reflect that.
The changes you have to make between champions are extremely minute, outside of utilizing an entirely different tree...which is why I suggested 6.
Also, no mastery gives you a reason to skip TP. Teemo and MF would never take TP anyway.
TP is rather unusable outside of extremely stupid plays from enemies that would have been punished hard regardless of your TP. The only exceptions are champions like Shen, a select few Juggernauts, and champions that would generally want to teamfight/engage, rather than split push, like Malph, Maokai, etc.
Outside of competitive play, you're much better off going with other summoners now in a lot of cases. A fight will more often than not already be over by the time your TP finishes, and that's not even considering the countless situations where you have to walk a little bit to actually get into the fight.
The nerfs hit it really hard. Its essentially only useful for forcing disengages and for adding pressure to dragon attempts now.
The masteries themselves are not better or worse than in the past as far as 'synergy', except that tank masteries suck complete ass. The only exceptions are damage Keystones, which are game-warping enough that if Riot wants to keep this game successful, they'll remove.
As far as runes go...there is no 'catching up'. You buy enough runes for two general setups. These general runepages work, and are more often than not among the 'optimal' rune-setups, for the majority of champions. They are not that hard to get. I hardly play this game and I have the majority of runes, and still lack many champions.
I, for one, am glad runes don't cost RP. That would just make it a paywall.
Runes have a marginal impact overall early game outside of extremely focused pages. 'Tuning down' runepages would be really, really fucking stupid.
Especially scaling runes. Scaling runes don't enable 'off-roles' in any way, shape, or form. Keystone masteries and continually gutted champions/itemization for intended roles do.