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That's an awful lot of Pokemon to befriend!
No, I never have, because I can't even make it through all of the dungeons, never mind working towards befriending.
I still play the first Mystery Dungeon game a fair bit considering how long ago it was released. I started again midway through this year and have befriended all of the Legends except two of the Regi's. Don't know if I'll ever befriend every single Pokemon though.
i came pretty close to doing so in red rescue, but never actually got them all. i'd imagine that if i was to, i would not erase my game file so often like i do today. When it comes to the more resent releases i don't think i would even attempt to. just a little too grindy for me.