I believe EB I-290 to WB I-88 will be eliminated. And honestly, who cares? Is that movement really needed? The vast majority of the traffic does not make that move, and eliminating it will allow for much better traffic flow for the primary movements. The few who need to make that move can continue down to Cermak/22nd St and take it west to the Spring Road I-88 entrance in Oak Brook.
It seems that it won't be. If you look at this screenshot from the presentation, you'll clearly see the split in the ramp from I-290 East, with one branch leading to to I-294 South and the other to I-88 West:

Here, the split is covered up by the arrow, as Brandon noted, but you can still see that the line representing the split is thicker in that area, which suggests that it is still there.

I'm not sure, though, how the three-dimensional geometry is going to work here. Which ramps are going to over or under the others? In my admittedly naive opinion, there doesn't seem to be that much space in the area to go up and down as needed.
As for I-39's "who cares" question, while I couldn't give the exact numbers, I can say that I make that movement fairly often, at least when I'm in town.