How have the Jays been vs the league at each position and are things improving? This is a big question for 2012 and beyond. Is JPA's 98 OPS+ enough for a catcher? What about Encarnacion's 113 OPS+ at DH?
Using OPS+ and sOPS+ via Baseball-Reference (sOPS+ is the OPS+ vs the split you are checking for the league, so if the average shortstop had a 90 OPS+ then if the Jays SS were a 90 OPS+ they'd get a sOPS+ of 100). I know there are better measures but we are looking for the obvious issues, not fine tuning ones, but Hill sized holes in the lineup.
Individuals are listed with regular OPS+ rather than split. Listing all guys with 10+ games at a position plus Johnson in order of games played (high to low).
Overall: 96 OPS+ (sub-par offense, scoring league average runs per game of 4.6)
CA: 108 (JPA 89 mixed with Molina's 111 OPS+)
1B: 89 (Lind 98, Rivera 80, Encarnacion 113)
2B: 70 (Hill 58, McDonald 70, McCoy 80, Johnson 32)
3B: 116 (Nix 49, Encarnacion 113, Bautista 191, Lawrie 181, McDonald 70, McCoy 80)
SS: 121 (Escobar 107, McDonald 70)
LF: 78 (Patterson 78, Snider 65, Thames 106, Rivera 80)
CF: 72 (Davis 67, Patterson 78, Rasmus 68)
RF: 138 (Bautista 191, Thames 106)
DH: 108 (Encarnacion 113, Rivera 80, Thames 106, Lind 98)
P: 19 (ugly, even for pitchers - 2 for 22, both singles, 1 walk, 10 strikeouts)
PH: 29 (Encarnacion, Rivera, Teahen have 5+ AB's, 7 for 42 overall)
So clear holes (sOPS+ sub 80) are 2B, LF, CF, and PH (and pitchers). Bad spots (sub-100) adds in 1B. Wonderful (120+) is SS and RF while 3B has actually been very good despite Nix playing so much.
Of note: for split OPS+ at 3B (what they hit while playing there vs the league average OPS+) you get Bautista at 229 and Lawrie at 199 compensating for Encarnacion's 92, Nix's 64, and McDonald's 42. In LF only Thames has produced a 90+ sOPS+ (100 on the nose).
So for 2012 what are the sOPS+ for the guys who will (likely) be manning the positions?
CA: JPA 102
1B: Lind 85
2B: Johnson 38 (97 for the season as a whole)
3B: Lawrie 199
SS: Escobar 122
LF: Thames 100
CF: Rasmus 70 (98 for the season as a whole)
RF: Bautista 176
DH: Encarnacion 130
This indicates that, if Johnson is resigned, only 1B is a black hole based on how the players have hit when playing their position this year. Clearing out deadwood that played often (Nix, Patterson, Rivera, Hill) makes a major difference. If Snider learns to hit at the major league level things can improve further. A big plus would be getting a bat on the bench as well.