[One Great Matrix]

As I can tell, the programme accounts for a pitcher's control from worst to best but there sometimes doesn't seem to be any accounting for the pitcher's rhythm...

If you study a pitcher's typical Real-Life game-log, I think you'll find that there are times when 80% of pitchers have very good command of their pitches...so that they might get in grooves where a walk is rather rare.

You also find the opposite where 85% of pitcher's are prone to little bouts where they walk 2 or 3 batters, or maybe 1 or 2 in fairly rare cases, runs in.
In the game it seems they might suddenly walk these 3 with the bases loaded + be left in to face another hitter where I don't think any sensible manager would allow more than 1 run to be walked in without pulling the pitcher in most cases. It's disgusting to watch.

Perhaps you could approach this from a statistical standpoint and see if the numbers hold up, to where the pitchers issue most of their walks during certain games or times in the game or situations or simply in these bouts or rhythms I'm referring to.

Or perhaps you could just add a sort of rhythm to the pitchers. A guy gets in a groove, retires 8 in a row, gives up a hit...then a couple walks & gets pulled...

Or a guy is mostly struggling, but gets a big strike-out or gets out of an inning, perhaps with a big double play, and finds his rhythm the next inning.