As yak says, the route through Abuja seems to be the most recommended route, but avoid going too far north.
Anyways, Nigeria is a pretty full on place but not as bad as some of the rumours would have you believe. Like all places, there are some rough characters but also some kind locals.
The biggest pain of the southern route was all the check stops but I seem to recall hearing that the stops along the road to Lagos have mostly been taken down sometime this year. They were there last year in December, not as much of a pain on a bike but in a vehicle, it would make for a lot of stop and go.
Coming from the south, one reason to go to Lagos was for the Burkina visa, which was some crazy amount if you got it at the border. Again there were discussions that they were going to reduce it to a more reasonable level that may have happened this year as well which would negate one of the main reasons to visit. Still, an interesting place to visit for the adventure seeker or if you know someone. Some of the local riders were exceptionally kind to me so I can't say enough good things about them.