It's rather plot strength. In Undertale, Frisk one-hits Mettaton Neo because they want him to get the f**k out of their way.
It's a one-hit out of spite.
Mettaton NEO is more difficult because you're afraid of what may happen to you, and aren't as prepared. Plot weakness, or lack thereof anything. Your [[Total Jackass Stunts]] are the reason this happened. You feel guilty because you aren't used to the genocide.