This is actually a very good point.
Like Pride, at least fights should be judged on their entirity.
This is not boxing which is called 'the sweet science' for a reason. This is meant to be the 'ultimate fighting championship'. It is to see who the best fighter is.
Then you get it taking the boxing scoring methods, where in boxing you have 12 rounds. Having the same system in MMA is stupid, a 1 point deduction costs you 33% of the points in the fight (assuming no 10-8 rounds) whereas in boxing it costs you about 8%. It doesn't make sense to apply scoring per round or you get stupid things like a guy going for a takedown in the last 30 seconds to score points.