Flames of War is a very good system. It's got a very good balance between game play and history. It doesn't bog down like a lot of historical games can. (If you've ever spent two hours while two guys argue over how fast a russian tank can turn around, you know what I mean.)
The midwar/late war divide is mainly in the points you pay for things. A tiger is a tiger. Use it in late war at 215 pts, or in midwar at 385. It's much more devastating in midwar, so it costs more.
US carries over very well mid to late. Germans less so, as they had so many upgrades continuously coming out, and a lot of the desert units were leftovers from other wars, or variations on what was available to them. Mid-war, especially Afrika, is probably my favorite time period.
I've got a few thousand points of US, 2000 in Afrika Germans, 4000 in late war Germans, and a bunch of russsians that I seem to have inherited/bought from 3 different people and need to figure out what I'm doing with them.)
We've got a 1750 Late War tournament coming up May 1st and 2nd. I won't be able to play in it, (possibly as a ringer if we have an odd number), but I'm looking forward to a ton of practice games with the guys who will be.