X was built with the Emergency Acceleration System (EAS, Dash) by default. It wasn't a hidden ability, just that he didnt know how to use it. The boots were merely training wheels. also, the buster differences are well, X gets more powerful when he fights. His buster ups itself. Remember Zero's words in X1.
"If you use all the abilities you were designed with, you should become stronger..."
in X1, X want at 100% of his default power yet. That includes not knowing how to use his EAS, and his weak power. The first armor was like a set of training wheels that helped him reach his 100%. afterward, he knew how to use his EAS unaided, and his charge shot became more powerful.
although in game, comparing X1 2 and 3, Im sure the buster does the same amount of damage each time, so its probably just aesthetic.