I like both. I love unique customs and styles, it's great to see for example persona pony collections with ponies from several artists -- it's wonderful to see each artist giving the character their own twist: there are as many different results as there are artists, yet still the character remains instantly recognizable. I also love to see artists who take ponies to the next level so to speak, some customs really are works of art! But I do love simpler customs as well, both original designs that follow the Hasbroish style and actual Hasbro customs, like replicas, alternate versions, gender or generation switches and so on.
In the end I think it really depends on the custom, and on the artist. I respect anyone who is able to create ponies that have the 'factory quality' look to them. Nevertheless, I prefer a more 'handmade' style myself -- I'm all for developing one's skills, so handmade is not an excuse for sloppy work. I'm constantly striving for smoother FBRs, for example, yet I refuse to buy an airbrush. Not every custom has to look factory in my opinion. Like most people, I don't like visible brush strokes, but I do like texture and a handpainted look, and the challenge of honing my skills.
The 'handpainted vs. factory' question is also probably somehow related to my preference for traditional art over digital; some people prefer the other way round. Of course there's huge variation between different styles within both media so this is just a rough generalisation, but I hope you see my point. Sometimes one style is just more suitable for a particular piece than the other. Same goes for pony customs. (Hope I'm making some sense here!
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