Kobe hit 3 pointers that were highly contested and often had the game on the line. Mike dropped 3's largely because his defender was scared of covering him within the arch so they let Mike shoot the 3 in an effort to not have him just take a 2.Their 3pt percentage was almost identical. Kobe made more 3s because, as you said, he played in a different era, which called for more 3s being taken. MJ played in an era that didn't rely on the 3pt shot. Even still, Kobe finished his career shooting 32.9% from 3, and MJ shot 32.7% from 3.
If you want to give Kobe the slight edge on 3pt shooting, fine... But I'd be curious to hear what these other "certain parts" of Kobe's game that were better than MJs... because I can't think of one.
Here's a good comparison: Kobe Bryant vs Michael Jordan: Who is Better?
Again, I prefer Jordan to Kobe, but it's a lot closer than many think.
I'd add, what I think shouldn't dictate what you think (and vice versa). So this is just my opinion. I appreciate your comments and perspective, but it doesn't mean I'm changing my mind.