But another way to look at it is that the parent with the magic pill may not think his child's blindness is a big enough deal to bother with giving him the pill.

That's not another way of looking at it. It's the same way. It still means that the parent wants their child to be blind. For, if they didn't they would give him the pill.

Maybe God doesn't think it's a big enough problem. Maybe He wants us to see beyond the wart. Or perhaps He can use that person to reach others who also have warts. Or maybe the wart can teach us humility.

Those are all explenations for possible reasons why God would want you to be a BL rather than changing you. They are all valid possibilities, but they are not alternatives to the fact that God wants you to be a bl, they are explenations for why he does. If any of those alternatives you present are true, then they don't take away the fact that God wants you to be a bl, they simply explain why he does.

Of course that brings us back to whether or not God WANTS us to have that wart. Kind of a chicken and egg scenario.

I don't see a chicken and egg problem here.