I'd go with the upper deck seats.
I've seen Cub games from nearly every area of the ballpark. From the 1st row behind home plate to the back row of the upper deck in both the left and right field corners, and just about everywhere inbetween, and another 20 or so games from the bleachers. I was just there a couple weeks ago and got my first taste of seeing a game from the new field level seats between the visiting dugout and bullpen, and I can't recommend those seats highly enough.
I'd take first row in the upper deck over 90% of the seats in any of the 200 sections. My tickets for Game 7 of the 2003 NLCS were in 512, in the very back row (I paid a good deal more than face value, but I prefer not to dwell on that).
I try to stay away from sitting too far back in the lower section, because the support pillars can obstruct your view, but it's really only a problem if you are sitting right behind one. Having been there as much as I have, I've pretty much learned where those sections/seats are. In the 20th row, from that angle, you might get the very last pillar on that side blocking your view of the plate, but honestly, I've never sat that far back in that section of the park, so I'm not sure.
If you can grab tickets in the first 5 or 6 rows in any of the 200 sections, you shouldn't have any problems with those pillars.