Waifuism requires a very specific combination of characteristics that Japan has down to a science, but the West has yet to really tap into as a market. Here are the elements present in MLP that I think a show needs to have in order to develop a strong waifuist following:
A predominantly female cast, with few to no significant male characters, is typically an element. The female characters usually have personalities that are distinct from each other rather than complimentary. The character personalities represent very general "types", which appeal to different men. This means that regardless of the type of girl a guy prefers, he can usually find at least one character in the show that appeals to him. With anime this is generally done on purpose to appeal to men, but with MLP I think the intent was to have each character represent a different general female personality that the young female audience could relate to based on their own personality. You have the glamorous girly-girl (Rarity), the shy, quiet, easily flustered girl (Fluttershy), the bookish smart girl (Twilight), the athletic tomboy (Dash), the bouncy, ditzy, funny girl (Ponk), and the hard-working serious girl (Applejack). If you go through Japanese dating sims or moe anime, you'll usually see some variation of most of these archetypes present in the characters.
The art style is also a significant factor. Neoteny figures heavily into the equation, because a waifu is not just a character you're sexually attracted to, but a character you form an emotional, protective bond with on some level. Studies have been done that show that females with more juvenile facial features (large eyes, large head, small mouth) trigger a protective paternal instinct in males. Female cartoon characters that exaggerate these features tend to have a similar effect. While Japan tends to design the majority of their characters this way, in the West it's a lot less common. Western female comic book characters, for instance, are usually drawn to look fairly true to life, with facial features and body proportions typical to a normal adult. While these characters are often drawn to be very sexually appealing, their designs don't trigger the same paternal/older brother protective instinct that is key to the waifu bond. You may want to fuck Poison Ivy, but she's not really a waifu.
The third and final element is that the story and setting of the series usually places the characters into generally safe, typical everyday situations. Moe anime series usually depict female characters going about their everyday school life, with very little happening in the way of action. Stories usually focus on the characters interactions with each other, their friendships, dealing with fairly minor, trivial problems, and generally just behaving like unrealistically cute girls. The male viewer is drawn into the purity and innocence of their world, and enjoys living vicariously in that world alongside them. He laughs when they laugh, cries when they cry; his happiness is their happiness, their sorrows are his sorrows.
With MLP, I think that all of this came together quite unintentionally. As I said I think the personalities of the characters were designed to appeal to young girls rather than adult men, the setting was just meant to be a cute, harmless pony world that children would like, and the stories were just meant to mimic situations that school-aged children could find themselves in. But, the designs of the characters were clearly influenced by anime styles, which immediately catches the eye of men who are drawn to that style. The charming, innocent stories and cute personalities of the characters combine with the protective/sexual instinct that the designs trigger, and suddenly *boom*, you've got a horse waifu.
