Alloy wheels are a really big improvement on the Varsity, since these particular steel rims are much heavier than all other brands of steel rims.
Varsity frames are pretty short front-to-rear, due to the frame's "slack" or "relaxed" angles. I always advise going for the biggest frame that you can fit on when selecting a Varsity or Continental.
Lots of other useful mod's for Varsities, modern parts like cabling, chain and freewheel, wider aluminum bars, padded tape, rubber hoods for the brake levers.
Also it's a matter of getting the bike carefully set up and fitted to the rider.
I did several mod's to this Varsity, and like you I really liked the color.
I should have chosen a larger frame size however.
I kept the stock crankset and kickstand because I felt that these are things that make a Varsity a Varsity.