Don't know much about the flying - though Air Mali/Malitas have given me a few interesting experiences - but I have spent a lot of time in Bamako. If you like Africa, Bko is great. Crime is reletively low, there are good places to eat (one advantage of a French heritage) and the music and culture are great.
If you are going to live in a hotel, try to avoid the Amitie - it's a big souless block near the city centre. The Mande is farther out, but it is much better - there are some newer hotels that I don't know about.
Driving is - how shall I put it - interesting. Watching a ten year old boy drive a cattle cart through rush hour traffic is always fun.
Medical services are not brilliant. There are a few good clinics but they are not very well equipped. Make sure that you have your innoculations up to date. I'd add rabies and various forms of hepatitis to the normal list (especially if you will be spending time outside of Bko). Malaria prophylaxis is essential in the south of the country (which includes most of the major cities). I use doxycycline, which isn't always reccomended by health authorities in Europe, but it has the great advantage of working.
Make sure you don't miss a trip to Djenne and Timbuctu (you've got to say you've been there). When you return, make sure that you watch the movie 'Sahara' it will keep you laughing for weeks.
Got to say, I'm jealous. Of all of the countries I've worked in or visited in Africa, Mali is my favourite.