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My guess on this is that this is plainly against the message pokemon wants to convey. This portrays pokemon as mere objects to do with as you please. I know the gameplay of pokemon itself is against this idea, and they didn't change that, but for some reason, this was a more obvious violation than that.
I will also note that Hacker's Memory has something that tackles this directly, and you are free to choose what you prefer. You can even choose to not pick a side. (although this invariably leads to you being screwed on using it at all)
Truly, I see no excuse to treating living creatures as objects, but not everyone is going to think as I do.
