Yikes.

I've always been a fan of the premise of the X-Men, I just think it's bullet proof as far as continuing narratives go, but the dual fact that the powers just came to them and that they were a problem to be managed, some with no solution (learn to succeed despite your limitations), was just the cat's meow to my teenaged brain. 

It would be fun to see a what if story where Scott has control of his powers and we see him without the glasses/visor.

Edited: Ok, it looks like the plane crash was first mentioned in "Uncanny X-Men" #144, so that would be Chris Claremont and during Dave Cockrum's second tenure on the title. A few years back, I reread all the issues of Uncanny X-Men in a short period, which is why I likely was confused if it was mentioned earlier than that issue.

I do find Claremont added some texture and depth to his comics by adding cool details and connections like this...but he would often go too far (everyone is related or in love or has powers...).

JB did a good job of reining him in. As did the great (again underrated as an editor) Roger Stern.

A mutation can be thought of as nothing more than a copying mistake in DNA.

Evolution is a numbers game, so as you say, if the random mutation gives an incremental benefit, once you go through enough generations, you should start to see increased numbers amongst a population who possess the benefit. Given enough time, the mutation becomes the norm. Then you may see another mutation that builds on or works with the mutation. Given more time, a beneficial such mutation once again becomes the norm, and so on, so that across very large spans of time very complex adaptations are possible.

A single step mutation like Cyclops' power is not realistic, of course, but that's OK. It's not the real world!