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It only has happened to me in platnum, because all my pokemon were traded from another game besides my starter. So like none of them listened to me in the begining.
None in Diamond or Platinum, but once in Sapphire I had to fight the Team Magma leader (can't remember the name) and I had all the low-level Pokemon I were training with me. I did pretty well, pwning all his Pokemon down to the last one. Then, my last stong Poke fainted and I looked to see who I had left in my party...
I had a Lv. 7 Poochyena with me... that didn't go over well. >.<
Yeah, It used to happen ALL the time. I really wasn't considerate of training any of my Pokemon except for Swampert, so it happened a lot, especially at the end.
Once I started to train all of my Pokemon it hasn't happened as much - usually when I battle the elite four I might lose to the Champion, but that's if I'm really not prepared.
It happened to me a couple of times on the old pokemon games. In the newer ones like platinum, diamond/pearl, I haven't though because I always keep a very good stock of recovery items with me.
Currently, in Platinum, 0. In Pearl, 0. In FireRed, 2. (Brock once and I can't remember the other time). Sapphire, 3 (can't really remember, though I think Juan was one of them. Liza and Tate may have been the other two). Those are the only games I remember.
I don't usually black out, I either have a few revives or super potions on me to keep my Pokemon healthy throughout the match. I used to black out a little more often in Yellow, Red, and Blue, though my battle losing rate has decreased greatly over the years as I use way more strategy.