Well, the new rotation code has min and max player requirements, but I guess that does nothing if the admin manually changes the map. I can't just remove those admin commands, though. They are kind of necessary, especially with matches. I think the problem lies in the admins, not the commands. Why is Dye32 an admin on Apex? You can always play on apex test -- no admins there to mess with it.
As for the cap ends round rule, why do you think it sucks? I think it's good for a few reasons.
1) Stops cap-on-the-newbie fests. I'm sure you've seen it. One newbie is left alive, hiding off in a corner somewhere, meanwhile the other team runs 5 or 6 caps before someone respawns or someone has mercy and kills the newbie.
2) Promotes teamwork -- it used to be one person would grab the flag and try to cap it, while everyone else would just sit in the enemy base and wait for the flag to return and make no attempt to protect the carrier -- he's on his own! Well, if the flag is unlikely to return to the enemy base, it basically forces people to provide support for the flag carrier.
3) Stops repeated 1v1 flag cap exchanges. Frequent on maps like arenaball -- the game boils down to two people running cap after cap until someone gets lucky and hits the other guy or someone forgoes the cap points and just goes for the kill.
4) Reduces spawn kills. As pointed out in #2, it's less likely that there are going to be hoards of enemy players in your base when you respawn. There is little less frustratrating than being killed the second you spawn because there are like 6 enemy players sitting around in your base waiting for the flag to return from the fifth cap run in a row.
Obviously it must be paired with the "flag must be at base" rule so it's not just the fastest runner who gets the cap.