I would expect the Rays would be #1, since usually the worst team gets the best picks. 10+ years of ineptitude should result in a farm system chock full of talent.
This is not really true in baseball. The MLB draft does allow the worst teams to pick first, but a lot of the top prospects hire Scott Boras as their agent and the smaller market teams shy away from his clients many times as they will ask for ridiculous signing bonuses. So many times teams like the Pirates draft a kid they know they can sign and the top talent falls to a big market team.
Secondly. Teams that lose free agents get 1st and 2nd round compensatory picks. So normally the big market teams that sign a lot of free agents every year and also lose a lot every year, get a ton of compensatory picks. For example, 2 years ago when the Rays drafted Evan Longoria with the #3 pick in the draft, they did not get to pick again until pick #58 and the Red Sox picked 5x between the Rays 1st 2 picks.
Also baseball has the highest bust factor in the draft. Many of these kids are drafted right out of high school based on potential. Pitchers have a very high injury rate too. So many of the best young pitchers get injured long before they make it to the big leagues.
Baseball farm systems are built with great scouting and having a great program and instructors throughout your minor league system. This is why under the old ownership, the Rays never even had their farm system rated in the top 10 despite having high 1st round picks. Many of their picks were busts like the Dewon Brazelton's of the world. The scouting was lousy and the talented kids weren't getting the right training to help them develop.
Here is the 2008 Baseball America ranking of farm systems.
1. Rays
2. Red Sox
3. Reds
4. Rangers
5. Yankees
6. Dodgers
7. Rockies
8. Braves
9. Nationals
10. Angels
11. Mariners
12. Padres
13. Cardinals
14. Marlins
15. Diamondbacks
16. Orioles
17. Mets
18. Twins
19. Indians
20. Cubs
21. Brewers
22. Phillies
23. Giants
24. Royals
25. Blue Jays
26. Pirates
27. A’s
28. White Sox
29. Tigers
30. Astros
Look at all those big market teams at the top. Great farm systems cost a lot of money to build. The Pirates rank 26th. How scary is that for them. The Yankees and Red Sox are in the top 5 because they can afford to sign any player, they get tons of compensatory picks every year and they can afford the best facilities and coaches.
When the new ownership for the Rays took over and they invested 10's of millions of dollars into building acadamies in Venezuela and the Dominican Republic people thought it was a waste of money and they should spend that on a bullpen. If you don't have a presence in latin America, you are never going to compete. We also have Japaneese scouts now that help us find players like Akinori Iwamura and Shinji Mori (who sadly blew out his shoulder his 1st spring here)
So I hope this helps you understand. The baseball draft is 50 rounds. And great systems are not build solely on 1st round picks. It takes a lot of money and a concerted effort to be ranked that high and it is nothing to be scoffed at.
Teams that reach the # 1 ranking on this list usually have a very high success rate in the 2-3 years following. The Rays are on the verge of making an unprecidented run as the #1 team 3 years in a row if they hang on to that ranking this year, which they should easily do. This ownership has not shyed away from the big bonus guys, hence us drafting Longoria and Price their 1st 2 drafts. The Rays are going to be very good for a long time.