1) I agree cap penalty would be better.
2) I think picks should only be traded for current draft and next year following. Two years out can damage a team pretty bad especially if the current owner resigns. I think picks should be eligible to be traded as many years in a row as possible due to competition. Teams currently competing generally do not need top picks as much as current players.
3) Salary Cap- I say do either the median salary ($114M- 2015) or an average ($130M in 2016) I am fine with either, but if we use median it will cut the cap some. As a result I would wait a year or two so teams could be compliant. I think that average salary is a better method going forward.
4) Minor League Affiliates- It is easier to track players but we can do it on our own if need be (which I will in that event). It is a lot of work at the end of the year for the commissioners so if we keep it please do it early so they do not get slammed with 1000 requests.
5) I agree. It should take 48hrs and highest claiming team receives negotiation rights.
6) Lineup- MLB teams generally carry 13 position players and 12 pitchers. I think our lineup should reflect that. As a result, I like the current setup due to the realism. It also makes it easier for non playoff teams to move players at the deadline for prospects etc.
My new proposals:
7) Rule 5 draft. Players that are in the minors and not on 40man after six years service time become eligible to be drafted to 40man rosters of other teams. This will prevent top teams from stockpiling talent and essentially blocking everyone else for that player's career. It also allows the lower teams to pick up fringe guys who could play.
8) International Signing needs a tweek. I am new, but I looked at the transactions from years past. First bid has to be doubled as a 'discovery' charge. However, top 20 or top 30 players are already known. So basically, the first person who bids can lock out the other teams with say a $2M bid or so. I think top international free agents set by MLB, Baseball America, or one good source should not be subject to that rule. That allows all teams to be able to bid for the top international players. Some people work, have kids, etc and I don't think it is fair to essentially punish someone because they didn't hear someone signed first.
9) Qualifying offers. We should set a qualifying offer (same as MLB charge) to impending free agents. If that player is signed via free agency, the signing team has to give their first draft pick to the team losing the player (however, it is top 10 protected). In the event a team does not have 1st pick, then a 2nd round is passed. If a team signs multiple qualified players, then it gives the picks to the teams in chronological order to whichever player is signed first.