The armors purpose was to focus mewtwo's psychic abilities, because before that his use of his powers almost always ended in explosions.
Giovanni's smooth talking made him control Mewtwo
In my opinion: More focus=more precise attack.
And also, there is one thing I don't understand in M01. At first Giovanni was like "You and me are going to be working together" to Mewtwo. But then he went completely stupid and told him "You're a Pokemon. Human and Pokemon will never be equal".
Where did he lost his brain? Wasn't he aware that Mewtwo could kill him and destroy his hideout at any moment? If he wasn't so stupid, he could keep Mewtwo forever.
Yeah, which is why it's mega (Poking at the people saying megas look like digimon, since digimon just adds armor)
turns to these http://images2.wikia.nocookie.net/__cb20120130125415/digimon/images/thumb/0/07/GranKuwagamon_b.jpg/320px-GranKuwagamon_b.jpg http://images4.wikia.nocookie.net/__cb20090127181115/digimon/images/f/f6/HerculesKabuterimon_b.jpg
Neither have armor on them.
Turns to this http://images4.wikia.nocookie.net/__cb20090127185703/digimon/images/9/96/SkullMammothmon_b.jpg