In particular, I'm curious on the mastery reducing summoner's cd %, and Runic Affinity. For Runic Affinity, because blue/red buff durations have been decreased, I'm not sure if it's worth it. I'm not even sure if it applies to Smite rewards, such as golems and frogs.
Yes. All the yes. Also get the potion upgrades. Seriously, those masteries help a TON.
While I've not tried it in S5, in S4 it worked really REALLY well on Udyr or any other jungler that planned ot mostly split push objectives due to the insane mobility that tree grants. Again ... not certain about S5 yet.
I've heard good things about tank junglers such as Sejuani taking 0/17/13 masteries for early clearing. The buff duration, summoner spell cooldown, biscuits, MS, mana regen, and extra health potion really help out.
I've always done it, but I play mana hungry sustainless junglers-- having blue longer, mana masteries, and SV/LS makes a huge difference. I haven't even made any new pages for the new jungle. 9/9/12 works well as a general page for everyone. Some champs get more out of the SV/LS mastery than others, but I have yet to find anyone who straight up COULDN'T use it.
I play without potion upgrades. I suppose that's personal choice, but it is another point.
How about an 
? Longer buffs, shorter smite, more movement speed + LS if you pick it up.
It's not terrible. Really just comes down to the champion and personal preference.
