How about we compare the Twins drafts to the Red Sox draft since 2000:
2000:
Twins (31) - Aaron Heilman, didn't sign and compensation pick
Twins (342) - Jason Kubel
Red Sox (62) - Manny Delcarmen
Red Sox (332) - Freddie Sanchez
Red Sox (872) - Kason Gabbard
2001:
Twins: (1) - Joe Mauer
(77) - Jose Morales
(377) - Kevin Cameron
(857) - Nick Blackburn
Red Sox: (48) - Kelly Shoppach (note, Boston didn't have a 1st round pick - Ramirez)
(243) - Kevin Youkilis
2002:
Twins: (20) - Denard Span
(61) - Jesse Crain
(152) - Clete Thomas
(182) - Pat Nesheck
(242) - Adam Lind
(332) - Evan Meek
Red Sox (57) - Jon Lester (Didn't have a 1st round pick - Damon)
(238) - Brandon Moss
(1342) - Brian Banister
2003:
Twins: (58) Scott Baker
Red Sox: (17) - David Murphy
(32) - Matt Murton (supplement pick)
(114) - Papelbon
2004:
Twins: (22) Glen Perkins
(481) Matt Tolbert
Note - Twins had 4 comp/supp picks in the 1st round. 5 first round picks, not a single real hit.
Red Sox: (65) Dustin Pedroia (No first round pick - Foulke)
(185) Cla Meredith
2005:
Twins: (25) Matt Garza
(73) Kevin Slowey
(84) Brian Duensing
Red Sox: (23) Jacoby Ellsbury
(42) Clay Buchholz
(45) Jed Lowrie
(47) Michael Bowden
Note: 4 comp/supp picks in the 1st round. 5 picks, 2 hits, 2 prospects, 1 tbd
2006:
Red Sox: (28) Daniel Bard
(71) Justin Masterson
(83) Aaron Bates
2010 Top MLB prospects:
Twins:
18 - Aron Hicks, OF
49 - Kyle Gibson, RHP
61 - Ben Revere, OF
62 - Miguel Sano, SS
94 - Wilson Ramos, C
174 - Deolis Guerra, RHP
183 - Danny Valencia, 3B
190 - Carlos Gutierrez, RHP
Red Sox:
20 - Casey Kelly, RHP
50 - Ryan Westmoreland, OF
53 - Michael Bowden, RHP
63 - Lars Anderson, 1B
69 - Josh Reddick, OF
101 - Ryan Kalish, OF
110 - Jose Iglesias, SS
150 - Reymond Fuentes, OF
153 - Anthony Rizzo, 1B
186 - Oscar Tejada, SS
195 - Junichi Tazawa, RHP
I'd say the Red Sox have done at least as good as the Twins, I'd argue they did better considering their far later draft positions and less picks.