This doesn't encourage as much as we think.

“We’re really proud of you Johnnie, for raising your grades this term. But if you had worked harder on your algebra, the results would have been better.”

Johnnie might feel encouraged until he heard the word “but.” He might then question the sincerity of the original praise.
This could be easily overcome by changing the word “but” to “and.”

“We're really proud of you, Johnnie, for raising your grades this term, and by continuing the same conscientious efforts next term, your algebra grade can be up with all the others.”