I do agree that if you've replaced the symbol then repainting the eyes adds your finishing touch on the custom. Lots of us aren't as good as others and even when we think we suck it turns out that really others see it differently and think it's brilliant...
My very first eyes were terrible but with practice they have definitely improved.
I really like that when you look at the eyes you can tell who made the custom, it adds that little bit of "I did this not Hasbro!" to the completed artwork.
I draw them in the sketch book when i design the symbol layout that way I can see if I like how they go together. I always draw them on the pony very lightly with pencil as well so I can work out getting the lashes to match and the pupils the same size.