While no expert, I definitely am familiar with stock system.. it is actually brutally simple system:
1) AFF_GROUP is set on Sam and Bob
2) Sam is following Bob? Then they are groupped.
That is honestly, basically all stock is. If Bob has army of 20 dragon-slaying friends following him, and Bob is eatten in the first round, then the group is instantly disbanded in stock code (see rule #2 above).
* There is no limitations that I am aware of in either system with numbers, nor whether NPC or PC.
* Group vs Group combat, only difference in the systems is stock system, leader dies, group is done. Anything else relevant that I am not thinking of?
* Charmies of any sort, whether companions or just charmed-mobs, all are handled in a different, but similar fashion as stock groups: Is horsie AFF_CHARMED and following Bob? Then he is Bob's charmie. As far as changes in a codebase, both the stock system and Vatiken's will behave the same I believe (except in Vatiken's system, if you are groupped and summon a monster with a spell through mag_summon() the pet will auto-join your group)
* The stock group system was not done right, in my humble opinion. So far Vatiken's system is superior in every way (once again, in my opinion).
I highly suggest just throwing up a stock codebase, throw in his group patch (there is a small bugfix he posted recently) and test it out though