NOOOOOO...
LOL...I actually liked the capitalization in the games. Makes it feel more like a 1016-year-old kid teen yelling every person, place, and thing on their excursion. :D It makes everything feel important! Though lowercase letters are a bit easier on the eyes...
I haven't started my "permanent" Pokemon files yet (and I am still stuck in Generation III >_>), but I've been following the pattern of just leaving everything in their CAPITALIZED! formatting. Except the thing is, I don't nickname legendaries (and I consider Lucario and Zoroark "legendary" for certain factors, even though they aren't officially)...
So for the nicknamed Pokemon with capital letters from past games, are they going to stay that way or get forced to first-letter-capitalized-and-rest-of-letters-are-lowercase (I'm thinking there's a noun for this...CamelCase isn't fitting the bill..). I assume they'll remain the same, but with the changes to "proper" capitalization, they'll look a bit awkward in Generation 5...