Why was the flag cap honor removed? Because people weren’t playing BGs the way you wanted them to? Because players created their own objectives instead of adhering to the battleground objectives?
You allowed people to take advantage of these bugs and then fixed them. Now their time is free to grind arena, professions, gold, raids, etc creating a compounding affect which will take ages to catch up.
It’s too late to do anything about the prepatch, but you need to reinstate the honor for flag caps. Who cares if people aren’t playing the BG the way you want them to. Let people play the BG how they want to.