What's with all this phasing wank? From what I understand, it's an ability that grants limited invulnerabilty, not some super ultra mega hax that makes Meta Knights 10,000+ years of experience impotent. MK also probably hits harder and can take more of a beating, has more superhuman abilities, is a smaller, faster target, (speed wise), and knows the Halberd, which is where they are fighting, far better than Shovel Knight. Meta Knight made the Halberd. Transmutation isn't going to work on MK, due to his resistance to reality warping, and finally, is bloodlusted. He stops attacking, normally, when his mask is shattered. Here he has no such restriction.
Meta Knight takes this by just being stronger, tougher, more agile, more experienced, having superior hax (electricity beams, regen against flesh wounds), having the terrain advantage (stated to be on Halberd, a vessel MK knows how to operate, and knows the layout of,) and basically just godstomping even though they're both 7B.