The difference is that the Mobile Suits were,

a) Harder to control, since ZAFT developed the technology only Coordinators could pilot them with any sort of efficiency, though later the EAF (Kira wrote one for Orb) created a 'Natural Friendly' version of the OS.

b) FAR more manouverable and can carry heavier armaments and armour, this is why one Mobile Suit is rougly equivelant to 10 Mobile Armours (which is why the Lucrasia Class Ship only carries 5-7 Ginns, where each EAF battle ship carried in excess of 40-50 Mobile armours.)


Note, though, that the Mobile Armous I am talking about are those stupid little Mobius things that can't do much - there are also Mobile Armours that utilise Mobile Suit technology, like the big crab thing that attacks shin and the centaur thing that guards the positron cannon in the desert. Some Mobile Suits even transform into 'Mobile Armour mode' where they no longer resemble humanoid forms (losing manouverability) but gaining other nice features.

In the end, it raelly boils down to their shape, humanoid shapes are 'suits' because we wear suits, all other types are 'armours' because while a suit is shaped to fit, armour can take any shape or form.