I do not get the strategy between magnezone prime/regirock legends awaken?

It's faster. Magnegatr forces you to setup two stage-2's, while Kraken (Magnerock, whatever) is only a single Stage-1 and a Basic Pokemon. With that, it also gives more room for extra techs, draw cards, etc. On top of that, it can abuse Kraken can abuse Magnetic Draw better than Magnegatr.
 
Not just that. Magnerock is much more consistant, and doesn't die to power lock as much. Lastly, if your Regirock is pulled out by luxray and knocked out, all you have to do is play another down, while with MagneGatr, you have to play down an entire Feraligatr line, which is much harder to get out the turn after its knocked out.
 
I tried to run Fraligator prime in my magnezone prime deck,
and it is very fast and very effective.

In magnegatr (magnezone\fraligator) you just run 3 rare candies and it runs very fast.Plus,you don't need to discard anything.
 
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