I wrote this last year, but still applicable to MLB '12.
I find that a developed game plan is always more productive when attempting to increase one's skill rather than just 'playing around.' I wanted to share my process for utilizing the batting practice modes.
As a note: I don't use timed hitting - I prefer analog.
Batting Practice Mode
I usually select a pitcher with a FB in the mid to high 90s with either a decent change-up or curve-ball/slider. I want to mimic the type of pitches I'll see in a game and more importantly the pitches I have the hardest time hitting throughout the course of a game.
Modes that I find most useful
Timing: This is the 1st mode I choose because the pitchers is going to throw every pitch in the strike zone. I can just get a feel for his FB and off-speed pitches. Once I start ripping getting mostly successes then it's time to move on. I personally like to have 13-15 successes before moving on. This is a good number that shows me that I'm picking the ball up well out of the pitcher's hand.
Discipline: Now that I'm comfortable with my timing, I want to work on my plate discipline. I have a tendency to swing at borderline pitches with 2 strikes and I'm of the mindset that I'd rather strike out looking than swinging on a ball out of the zone. I don't really gauge my success based on the number provided in the game, rather I gauge success on how many pitches I was thrown during a session. I want to see 35-40 pitches in one session before I'm comfortable moving forward.
Good At-Bat: This is my favorite mode in batting practice. You get to take the timing and discipline you worked on and test in a game situation without actually playing a game. I also use this mode to look for pitches in my 'happy zone' which helps me to take pitches that are outside of that zone. I'll sometimes get into a mode where I want to swing at ANY strike pitched my way. Unlike discipline training, you won't be penalized for taking a strike (unless it's the 3rd strike). Sometimes a pitcher hits his spot and there's nothing you can do about it, so I'm waiting and betting on him to make a mistake so I can crush the ball for a screaming line drive. I know when I have a good at-bat without the mode telling me, so I will usually leave this mode when I feel comfortable with my at-bats.
Modes I don't utilize
Contact: I don't find contact training to be useful for timed or analog because success seems to be based on placement of the PCI which the user does not control in either of those hitting modes. I've had many solid contacts that have resulted in fails when my PCI was not squarely on the ball. (I'll post pictures if necessary).
Pitch Recognition: I personally don't use pitch recognition because I can do that training in 'Good AB' mode by sitting on a pitch. I would find this mode useful, however, if I was training myself to look for pitches in certain locations. I think the training mode is ideal for that.
Those are the 3 modes that help my batting out, especially if I haven't played in a day or two. Hopefully this will help you develop your own hitting plan for making batting practice mode more productive towards your goal of becoming a more complete hitter.
They hang 'em, we bang 'em. Happy Hitting fellas!