I'm startnig to think that Ninja-toolbox is the way to go.
Run 4x Higure, who acts as both your ninja-fetcher and an evasion supplier.
Then you can run single (or double) copies of specific control-based ninjas, like the Mistblade, Deep Hours, Okiba-Gang, Skullsnatcher, Throatslitter, and Ink-Eyes. Let's say you run 2 Deep Hours, that gives you 11 ninjas total.
Supplant the ninja-based control elements with 187 creatures that fill the voids in the deck (land fetching, art/ench destruction, etc.). Let's say you run 12 187 creatures, now you are up to 23. That theoretically leaves 13 slots to clean up the rest of the build, which should be plenty.
With potentially very heavy creature-control elements in place, I feel the tempo-loss associated with the ninja mechanic would be largely negated. If they can't keep creatures in play, then it is likely they cannot establish any tempo. The continuous damage of the ninjas finishes the job.