One of the questions in the rebuild will be the next CBA. Theo and Hoyer several times mentioned that cba changes really curtailed their intended process with the previous Cubs rebuild. They got Soler signed before things changed. Bit then the concept of investing big in draft and IFA (while perhaps spending less on the big-league roster) was taken away. The loss of draft picks for signing good FA's was also a factor; for signing Heyward and Zobrist, they lost their top two draft picks in 2016. (Michael Rucker is the only pick from that draft to reach the majors, Tom Hatch was the Cubs first selection.). Because the CBA had removed draft compensation for players traded mid-season, they were able to sign Lester without losing their pick in 2015, which resulted in Ian Happ. Subsequent changes made it so that even had we held onto Baez/Bryzzo, compensation picks would be a round later than in days past.
Hoyer is not wrong to acknowledge that it's difficult to know exactly what options will make sense without knowing what the new CBA looks like. Do you want to sign FA's to make next year more competitive, while costing draft picks each? Will you be losing your top pick, or only subsequent selections?
My guess is that the union itself doesn't care too much about IFA or the draft, so long as teams are prevented from diverting big-league salary to amateur procurement. So I'd guess the players won't have much motivation to change the draft or IFA. So, good chance that there will be some modification to the current system, but it might not be very radical.
There has been talk of instituting an IFA draft. Between the two parties, I'm not sure which side would push very hard for that, though? Maybe some of the smaller-market owners, wanting better parity? That's been mentioned often, but I'm not sure of all of the things the two parties care about economically, I'm not sure IFA-draft would fall within the top 100 issues for either side. (And probably even within the owners, there'd likely be divergent views on that.).
From the players side, one small modification that I'd suggest would be to remove any draft-choice penalty for teams who sign FA's. Players know that a rebuilding under-spending team like the Cubs has a conflict. We want to sign FA's to get better; but we value draft picks as a way to get better, too. Penalizing and disincentivizing the Cubs for signing FA's does not encourage them to spend, or to even make competitive offers that drive up offers. There was some penalty-moderation in the last CBA, I think, but erasing any penalty would make sense to me. That would make it easier for a team like the Cubs to use BOTH draft AND FA to rebuild, and I don't think the Cubs are unique in that.
I still think there is competitive-balance reasons to retain some level of compensation picks. if you lose a guy, get a comp pick; but don't penalize the team who signs a FA. That would be best for players and spending, I think. Personally I almost think bringing back comp picks after the first round instead of only the 2nd might actually benefit both competitive-balance and perhaps do the players as much good as harm.