Posting this from my phone, sorry for any spelling or grammar errors.
To me, the Blue Jays have done a lot of things right since Alex Anthopoulos took over as the GM.
1. They are widely regarding as having one of the best farm system's in all of baseball.
2. Acquired Colby Rasmus for hardly anything from the Cardinals, using bullpen depth to do so. Yes, he's hitting in the 220's, but when he was healthy and playing well earlier this season, he looked extremely dangerous in the Jays lineup.
3. They acquired and developed Jose Bautista properly, something that no other team could do. That includes the Tampa Bay Rays, Baltimore Orioles, Kansas City Royals and Pittsburgh Pirates.
4. Unlike the JP Ricciardi regime, the Jays won't rush prospects anymore. Everyone is being developed the right way and that's a huge positive for the future.
5. Acquiring Brett Lawrie for Shaun Marcum will end up being probably AA's best move. Lawrie is having a bit of a sophomore slump, but he's still getting on base and I know the power will come.
6. Putting Casey Janssen in the closers role was a very smart move by Farrell. Janssen is a guy I've always liked and his ability to use all of his pitches and throw strikes has turned him into a dominant closer. I think it would be a mistake to give the job to Sergio Santos next year, Janssen has earned it and looked really good as well (20 SV, 2.67 ERA).
7. Acquiring Edwin Encarnacion for Scott Rolen: Well, you know the story of this one. Much to his credit, Encarnacion has worked hard on developing his game so that he can have a better approach at the plate. More to the Jays credit, they never gave up on him and now he's a premier slugger in the American League. If you think this year is a fluke, you are very wrong. This is his upside, a 40+ homer, 100+ RBI guy.
Having said that, there are things AA did I really don't agree with.
1. Trading Aaron Hill for Kelly Johnson: Hill wasn't healthy, he had a few rough years but he still had that power second baseman upside which we saw once or twice while in Toronto. Johnson was known to be a guy that hits for a very low average and plays mediocre in the field. I can't stress enough how much that hurt the Blue Jays. Furthermore, Hill was a very likeable guy and one who I think was a leader that they sorely miss.
2. Shying away from Prince Fielder: AA and the Jays had the money to sign Fielder, but they chose not to because he wanted a long term contract as opposed to a few years at a high salary. Fielder is a leader and he would have been amazing protection for Jose Bautista. Put together the fantastic season Edwin Encarnacion is having and you have an amazing 3-4-5 combination if the Jays signed Fielder. You could have DH'd Encarnacion all year and signed Fielder. Its not a coincidence that Ryan Braun won the MVP while Fielder was with Milwaukee and now Cabrera looks like he may win one this season.
3. Going into 2012 with the pitching rotation he had: Not for one second did I think the Jays pitching would be a huge strength of the team. I had no idea Ricky Romero would be this bad, but there's a reason for it. If you didn't notice, veteran hitters have stopped swinging at his changeup because it has so much movement on it and never seems to be a strike. His trust and command of that pitch is essential, but overall his command has not been good this season and he walks way too many hitters I find. You can sit there in the front office and say "If Henderson Alvarez can put it together" and "If Kyle Drabek can become a viable starter" or you can take action. The Jays could have traded for pitching, but they decided to stick with what they had.
If the Jays want to improve, they need to do the following.
1. Go after a second baseman and top of the line starting pitcher.
2. Leave Casey Janssen in the closers role.
3. Trade Yunel Escobar (give Adeiny Hechavarria shortstop).
4. Adam Lind should not be a regular, he should be a bench player.
5. Go after some veterans, clearly they don't have enough leadership as is.
6. Rajai Davis is a utility player, you need a better left fielder than him and a guy that can get on base or provide some power.
7. Let Farrell go to Boston, because the story wouldn't keep coming up if he wasn't thinking about it.
That's just my take on the Jays, great discussion going here.