I'm not really bothered by the fact that there's only one save file. I was way back when I first started playing and my brother and I had to share Pokemon Red but ever since then we've just picked up our own copy. And because we did, we've been able to trade back and forth when needed. He doesn't play anymore but the sentiment is still there.
I don't get how nicknaming would have any effect on it, though...? That's kinda weird but maybe there's something I'm not thinking of.