The new player agreement changed the rules for free agent compensation. The temporary changes this year probably work to the Twins advantage. They will get a supplemental choice in compensation for Capps without offering him arbitration. And its likely they will still get the same draft choices for Cuddyer and Kubel.
The permanent changes are bit more dicey. In order to get compensation a team will have to offer a guaranteed one year contract at the average salary of the 125 top paid players the previous year. This year, that would be slightly over $12 million. That would be the third highest salary on the present Twins after Mauer and Morneau. The Twins would not have made that kind of offer to any of their free agents last year. Cuddyer is probably the only candidate from this year.
It appears, the compensation was changed to only include a supplemental draft choice after the first round. The new twist on this is that it appears the signing team will have to forfeit its first round choice if it is not in the top ten (they forfeit their second round choice if it is), instead of giving it up to the team being compensated. This means those supplemental choices will all move up a notch every time a player is signed. That seems convoluted, so maybe I am just misreading the reports.*(see update below)
The bigger issue is that there will also be a drawing for supplemental picks for teams in low budget and/or small markets. The Twins are no longer in that category. There will be a budget for both signing draftees and for international signings based, in part, on the previous year's standings. If a team goes over that budget, they will be penalized both financially and by losing draft choices if they go over by too much. So successful teams will be placed at a disadvantage in several different ways when it comes to drafting and signing players. For the Twins, whose model relies on player development, this will be a much bigger hit than for teams that look at prospects as little more than trading chips.
Of course, that assumes the Twins continue to be successful, if they aren't some of the new rules would work to their advantage. But the ability to sustain success through the draft and player development has been made harder. Ands that is not a good sign for the Twins.
The process for dealing with the forfeited draft choices is actually even more convoluted than I described. They will be put into a lottery in which all teams who have not gone over budget for signing draft choices are allowed to participate.