Just an update to this article:
I ran Yanmega Magnezone with great success this past BR's, going 6-0 in swiss, only losing games 2 and 3 in the final match against my worst matchup, Zekrom. (Both Donks)
I still believe it's a top tier deck, and would argue it's still the most consistent deck in the format (magnetic draw is insanely consistent). My list is a lot different than the one I originally posted, however, opting to max out the pokemon lines and key components of the deck's engine including junk arm, judge, etc. Like many have already said, I believe the best way to run it is without techs outside of Pachirisu for the energy acceleration. No tricks, no kingdra, just straight consistency cards to maximize the chances of drawing a rare candy + a way to get Magnezone for T2.
My basic Skeleton list looks like:
4-4 Yanmega
4-2-4 Magnezone
1 Pachirisu
1 Cleffa
4 Rare Candy
4 Junk Arm
4 Communication
3 Catcher
2 Switch (2 is a MUST, I don't care what anyone says. It's never a dead draw and you don't want to have to wait for that single copy at the bottom of your deck if you only run 1.
xx trainer tech (PlusPower, Lost Remover, Max Potion, etc)
4 Pokemon Collector
4 Judge
xx Shuffle draw/straight Draw
10 Lightning Energy
55 cards total
5 spots left do do whatever you want. More energy is nice. I'd also recommend 2-3 more shuffle draw cards and a tech against ZPST, since it's your deck's worst match up. A Lost Remover would work here, or an extra copy of catcher or whatever.
The point is the meta has changed back to base set where THICK lines of basics are required. 3-1-3 is asking for trouble, especially against a meta with catcher and trainer lock. Your list should be built with one goal... T2 MAgnezone. Once you get a few out, the deck flows like wine and you're going to be able to draw almost anything you want.