BV - I was in a similar situation to you when my unit introduced FDM .The mindset you're in is "what would I think is important to look at" and obviously rotate speed doesn't make the cut.
The misunderstanding is the mindset there - you don't look at what's important, you look at literally everything on the aircraft that has a limit or rule that has any chance of being machine processed.
The challenge on a unit that flies dynamically rather than procedurally (FJ Vs multi as an example) is that last bit. For example, FDM would never be able to tell you that you were using too much or too little G in BFM to get a shot, but it could easily be programmed to recognise someone routinely using more G than the Sqn beefer is comfortable with on a VRIAB.
We had basically every parameter from the ODM, RTS and FOB looked at, plus all "standard" profiles that could be automatically analysed. The FDM provider was helpful in that regard. Even ground taxy speed was included.
All of the above said, I've yet to ever actually see anyone get booked by it, but I can conceive how it would have picked up the trend of underspeed rotating - the key is in looking at every bit of performance data and limitations/rules that you use when you fly, whether you think it'll be broken or not - it doesn't cost extra!