Non-folding bikes are not allowed on the Chicagoland Metra trains during any of the times that I would be commuting. I thought long and hard about a folder, but the train can get pretty crowded, and although it would be technically allowed to bring it on anytime, I can see a folder becoming a bit of a hassle to lug around all the people.
I just got lucky that the train station that was most viable for me ended up having bike lockers. I don't believe that the majority of Metra stations have them.
One other suggestion: If you do end up using two separate bikes, consider setting them up so they use much of the same kind of equipment. For example, if you are commuting when you will need lights, think about how you will be needing to take the lights off one bike and put them on the other twice a day. You will want to do it quickly and with minimal trouble and it's nice if you don't have to carry two separate light setups.