with regards to Aguinaldo killing off his rivals, i think it was because of rivalry on who will lead the revolutionary government.

he had andress bonifacio killed because gat andress led one of the biggest factions of katipuneros. an illustrado like himself could not bear the thought of an indio leading the revolution. btw, gat andress loss almost all his battles due to poor planning and execution. but damn the man was brave!

he had antonio luna killed because antonio luna was winning more battles than him, and thus presented a rival for the leadership (mas pogi!). antonio luna was the only general of the revolution who studied military science and thus was good at tactics. he was also the only general who taught his men how to shoot their rifles. most katipuneros would remove the rear sight of their rifles because it was "storbo", gen. luna showed them it's proper use. he also taught his men correct field tactics, like how to attack or retreat in formation and by companies. one american company commander even said that he had not seen such markedly good disciplined soldiers in his carrer during an encounter with antonio luna's men. this basic training led to better results in the battlefield.