Not sure what changes you can make other than hope guys like Schwarber and Happ get better. Maybe Contreras also, and hope Bryant gets back into form. Not sure who will be available in free agency. Well Harper and Machado are the biggies but that will entail breaking the bank.
Here are the questions I have, having thought about this overnight.
Starting pitching: I'll assume that Yu comes fully back. The question is, do you pick up Hamels option? I am thinking yes at this point but if they do, can they afford to sign another big name position player? If no to Hamels, what do they do with Chatwood? Do they try to reclaim him somehow or do they dump him? Will they look to trade position players to get another starter?
Relief pitching: I will assume Morrow makes it all the way back. While I like the ERA from the guys overall, I am not sure they have enough "swing and miss" in them as compared to other pens (Milwaukee a prime example). Edwards has some when he can find the zone and Strop does as well. Wilson, too. But they aren't flamethrowers like other pens are. I'd like to see them shore it up a bit. I don't think they need major changes but a couple of tweaks should be good. I have no idea who's available so I cannot even comment on who they should pick up.
Position players: The biggest question to me is Kris Bryant. Is he going to be healthy enough to play at 3B or do the Cubs see him as an OFer due to his shoulder? Putting him in LF will definitely help his shoulder but guys would have to be moved out (one of Schwarber, Happ, Heyward or Almora). If they see Bryant as an OFer, then signing Machado to play 3B makes sense, assuming they can afford him and keep under the luxury tax (since they have said they want to stay under). If Bryant stays at 3B, I don't see them being a real player in the Harper derby due to the fact it would put them over the luxury tax cap (pending shipping guys out like Heyward, for example).
Also, what to do about Russell? Are they going to keep him (suspend him) or will they release him or trade him? I think Bote has shown enough that he can handle 2B so I could see an infield of Machado, Baez, Bote and Rizzo if they decide that Bryant's position is OF. I think Russell's admin leave ends today so perhaps we will hear something about that soon. Not sure which Russell is the real Russell. Is it 2016 Russell or 2018? Time will tell of course but assuming he's in good standing with the league, his defense alone should be enough to get something in return for him should they want to trade him.
I am disappointed at the end result but overall, I thought it was a pretty darn good year for all the stuff they went through. Hope the guys rest up and they get ready to bring it in 2019.