Earlier quoted context omitted.
I like to say something like "Hey, I realize you put a lot of hard work into X, but I think Y would be more efficient and save us all time in the long run!" Because then you're being totally truthful (assuming they actually are putting in effort) while still not coming across too directly.
"It's impressive how much time you were able to waste while only accomplishing X", but said a lot more politely.
Praise should never be a time to display your intellectual superiority.