Excellent overview Jim.
It took IS/TN a couple of iterations but it eventually got to the point where it things are manageable. The manual ack point is a great one. FA stuff in general has been a relatively weak area. I remember a version where acking to the transaction set level wasn’t something supported out of the box–“left as an exercise for the reader since transaction sets were inherently partner/implementation specific.” They were really wrong on that one.
I’m trying to remember if I was one of the folks that said that partners should always send an FA. I’m not sure if I did. 
But your point about this reminded of another rule of thumb–be prepared to accept transaction sets from partners that use codes that are not part of the version/release being used. Or not even defined by that particular element in any version. This practice seemed more prevalent with EANCOM to me but perhaps I just hit the jackpot with partners that liked to mix and match! To do this means controlling validation with the TN processing rules.
Regarding the batching we had discussions about, I see that in a later version (6.5 I think?) that the enveloping services now allow you to specify “leave my control numbers alone” which was one of the options you wanted to have. Perhaps you were the reason for this update?
Anyway, good post. I’m sure people will find it helpful.