I prefer text that reads more naturally, so I'd normally avoid allcaps keywords in favor of standard sentence case. That said, though, the allcaps does have a certain old-school charm to it, so if I were ever to work on an older-gen project I'd probably go with the allcaps for that retro touch. (Really, given the fonts used, the capital letters usually just plain look nicer in the interface imo.) Anything Gen III and newer just looks more aesthetically pleasing to me with normal case.
Of course, when I'm just writing normally (or in fanfiction) I actually treat things like pokémon and item names as common nouns, just like equivalent English words, rather than as trademarked proper nouns—pikachu, aerial ace, oran berry, just like mouse, triple axle, pineapple—so if I were working on something that wasn't supposed to look... "official", for lack of a better term, I might well just stick with that, at least in dialogue and such. (I figure species names in the interface would be more like proper nouns at that point, since you're actually referring to that pikachu as "Pikachu" and all.)
