Of course, the most likely villain to succeed in a world of magical pastel horses is the emperor which even magic itself obeys.
In G1, Grogar was so powerful an archmage that he could even manipulate and nullify
the magic of others. With how effortlessly he wields his own arcane might, and how he is effectively immune to almost all forms of magic himself, Grogar would claim the crowns of Equestria in one fell swoop. All ponies would bow to him.
It also opens a beautiful conflict with Twilight herself. How would The Princess of Magic handle the scenario? The most powerful archmage/necromancer/lich in all of existence stands before her, while her own magic betrays her
The power of friendship, and the Elements of Harmony betray her. All of it simply refuses to respond to her whims. Think of how helpless
Ah, but as the Element and Princess of Magic, I wouldn't doubt that she'd discover the loophole in Grogar's dominion over magic.
While I still prefer Tirek over Grogar as the top villain of the franchise, Grogar is a more appropriate villain to pit against Twilight Sparkle.