I do vaguely recall Lucas saying something to the effect of his reduced biomass (because, sans limbs) is the cause because it means fewer midichlorians...
Lucas never said the "because it means fewer midichlorians" part; that was added later in "whisper down the lane" style. Midichlorian count is a cell concentration as explained in TPM, not a total over an entire body; OT Vader thus would have the same midichlorian count as TPM Anakin. But there are other ways to impede Force use. Yoda may be naturally smaller in stature, but he's not cyborged, cut to pieces and on life-support. His statement about size was in context of the former as opposed to the latter.
They sure have done a great job of making him a huge pussy over the last 15 years and I miss evil Vader.
Try the Force Unleashed games. Evil Vader is all over that shiznit.