I'm late to the party but somehow I ended up here. I'm reteaching myself this now. I remember Captain Mench had a solution for this on the ProVideoCoalition site at one point for taking 60i footage and conforming to 24p using Shake. The key element was Optical Flow, Motion uses OF as you know. But I've just been doing a bunch of tests all night with some 60p (59.94) that we shot last week. The CrumplePop tut is the one I've been following for Motion 4 and some random youtube stuff using Time Warp for AE tests. The consensus seems to be each technique, including Twixtor, has limitations depending on the footage. AE better in one instance, Motion/Shake/Boris Red in another, Twixtor generally better than everything but still with flaws. Let alone the other factors like did you shoot 60p to begin with? Was the shutter 1/60 or 1/1600? Other great tidbits like this slomo conversion chartand this other Motion tut, 3 steps and bang! I gotta go to sleep, hope this helps.
Forgot this guy, of course he has some great tips from his friend on using Twixtor.