Well, there are few reasons for this.
1) After season 3 (correct me if i'm wrong) Lauren Faust was no longer directing MLP, so someone took this place, mb with slightly diffrent vision.
2) Let's be honest, they just relized that they missed the targetted group of viever and slightly changed the show becouse of that too.
3) also, the times are changing, some things are more demanded in TV now, some less. Today (even in cartoons) there is a lot of 'action', i think they found 'friendship lessons' a bit boring and moved to more spectacular things.
4) Animators improved too, compare same places in season 1 and (fe. 6) and u will see diffrence.
I know tobic was about look of ponies....but i had feel to write this :v