It's because they're making 26 episodes per year.
Movies typically take two years to make, and their final working time is about two hours of movie: 2*60=120 minutes in 2 years.
My Little Pony seasons normally have 26 episodes and are made in under a year, which are made according to the Digital NTSC Serial: 26*(23:00) = 598 minutes in 1 year.
So there's one reason.
The distinguishing factor between My Little Pony and many other animated television programs is, as always, due to the production style. Almost every company has their own method, which can involve varying degrees of hand-drawn work (digitally drawn or traditional), which will forever be a slowdown. But the effect of spending more time on animation is always quality.
If you think South Park and MLP have comparable quality in terms of how much you enjoy them, fair enough; I'm not talking about that kind of quality. I'm talking about technical competence, detail, extraneous "flavor" added in, which is only afforded through extra time, extra work and extra money, which ratchets up the production scale.
The Simpsons for many years was drawn and then scanned and digitized. Now, the Simpsons does what Family Guy did from their beginning: entirely digitized painting and drawing. The biggest seperation between Family Guy or the Simpsons from My Little Pony or South Park is that the latter two are not made in pure digital drawing, but in a form of Flash animation, using vector sprites. This speeds up some kinds of work but slows down other, and the main draw of choosing flash is that it facilitates a certain visual look which is difficult or impossible to do otherwise.
All in all, the simple explanation is that My Little Pony from the very start was given a very specific designed look, which requires a certain amount of time to make to a satisfactory degree. And the degree of quality which MLP has been made to, ever since season 1, has been increasing.