My understanding from riding both sizes is there is very little difference.
What the 49cc lacks in raw power, it makes up for by revving longer. Gear it lower.
and what the 66cc lacks in top end, it makes up for in grunt. Gear it higher.
Either engine can be improved substantially with careful porting.
But in the end, for MY money:"There is no replacement for displacement"
Why build a turbo 4banger for $25k when the same money will get a blown big block?
Same labor pays off better on the bigger engine.
But then again, I have no problem with lying my a$$ off to authority figures....
"Why yes officer, it IS under 50cc and therefore legal according to state laws"