If I play this deck again (currently fiddling with Nexus), I'm considering Temur. The elemental package is already semi-playable, and going Temur means both Omnath and Chandra. 6-mana Chandra destroys Nexus, is effective vs. Scapeshift, and helps against control, too.

Honestly, the strongest version of Manip rn is the Simic version with Leyline IMO. Elemental package other than Leafkin Druid/Risen Reef/maybe 1-2 Cavaliers is just way slower than that.

How do you beat Scapeshift with Simic?

Nexus....

Yeah, but that's not Manipulation.

Problem with Simic is that I don't see good sideboard cards against Scapeshift. Ashiok isn't much of a sideboard card - it disables like 8 cards from their deck, which slows them down but doesn't solve the problem of how to win after getting to late-game, which you are going to get to, since ramp doesn't kill very fast. Crafty Cutpurse works but it's only for one turn, and it's disabled by 3-mana Teferi anyway. Bant at least has Deputy of Detention. 3-mana Teferi disables their EoT-Scapeshift combo, and can potentially rebuy Deputy as well.