If you think hard about it, Hojo is one messed up person. Lets not even talk about everything with Vincent and Lucretia.
Killed Professor Gast, then has Aerith's mom and baby Aerith tracked down and the mom ends up dying. Preformed experiments and hints at breeding Aerith treating her like a tool. Almost held a survival of the fittest in that pod, but thankfully it was Red XIII and not some other animal.
Experiment on his own son, turning him into a super solider and creates the SOLDIER program but also turns people into monster due to excessive Mako poisoning.
Nibelheim Incident survivors - EXPERIMENTS! (Cloud and Zack specifically)
Himself - EXPERIMENT!
Edit- Oh Also all of Deepground.
Also just missing helping his son destroy the world.
I don't have a clue on how we could make Hojo any more evil, with the exception of ^JechtShotMK9's opinion.
Edit- However what would be more interesting is if we find out what leads him down this road. I am nearly certain that has not be explained in any part of the original game or compilation.