Not sure what color you're running, so I'll just run down the list:
: Most of your hard hitters are immune to freeze (so obviously you aren't an Aether player).
: Use Owl's Eye to destroy his squids.
: Drain Life his squids. You can also be sneaky and use Liquid Shadow on his squids. He'll get a couple points of health back, but it'll kill the squid.
: This color has more creature-destruction options than I'd care to list.
: Earthquake his lands to make that 3-quanta cost all the more punishing.
: Chaos Seed/Pandemonium to try and destroy his Squids. Also, Discord will make it hard for him to want to keep casting.
: Burn, burn, burn.
: Gravity Pull his squids to burn them down.
: As mentioned already, Adrenaline your creatures and they'll break-out much more quickly.
: You should easily be able to out-last him until he decks-out.
: Get your weapon out and start kicking his Squids back into his deck.
: Try to farm-up a few squids and use them to lock-down his squids.
Also, I know that you're talking about a Fractal deck, and a lot of these are single-target. The idea is to kill his Squids before he gets the Fractal out (because you know the AI isn't smart enough to hold a Squid in his hand on purpose so he can drop it and Fractal in one turn). Also, a lot of these cases will let you out-last him while your weapon whittles him down, especially if you're using a shield that renders all the Squids useless for attack.