I sort of apologize because this is sort of a double post (from the 7/25 game thread) but I thought this was the proper forum for people to discuss or comment on this matter. I didn't see the confusion that occurred during the aforementioned game but I think this shows that there is room to improve the system of substituting beyond an umpire writing it down. I would think that some type of electronic system would be available using I-pads or something similar that would enable the managers, the umpire, and the scorer to see and verify substitutions before play resumes.
I read that someone speculated that there may have been confusion between position numbers and player uniform numbers. For the purpose of scoring each play it's fine for the position numbers to be used in the scorebook. However, for the batting orders, lineups, and available bench players I think that uniform numbers should be the only stand-alone numbers used. For positions I propose using only P, C, 1B, 2B, 3B, SS, LF, CF, RF, DH, PH, and PR. The one problem about this is that it would be necessary to eliminate the Jackie Robinson tribute day every season. I have a ton of respect for what Jackie Robinson accomplished and I think it's fitting that 42 is a retired number everywhere but I think having every player wear 42 once a year is a bit silly.