Here is what ruins the Amiga versions for me -
Last Ninja 1 - quite good actually.. nice renditions of the music, decent graphics, ok controls... however, it's far too easy. The enemies don't even hit back if you keep hitting them rapidly.. not even the final boss! So that is a huge drawback about this port.
Last Ninja 2 - horrible controls, crap graphics, ugly sound, slow, terrible, rubbish!!
Last Ninja 3 - I heard this was the only one done inhouse by System 3. It's actually not bad.. the trouble is how they changed the controls! They're completely different from in any other Last Ninja game (LN3 for the C64 has normal LN controls).
They added some extra stuff to this version - an extra level, end of level bosses, a bigger last level, more puzzles and... Kunitoki (the final boss) is a robot (I'm not joking!)
None of them are anywhere close to the C64 versions though in terms of playability.