@MikeLovesRabbit One way to solve that is to reduce the pick up time. Currently Zarya is useless in CTF. Her barrier doesn't last long enough to pick up the flag. With teams split between two points there isn't a concentration of damage to keep her in high energy, and a lower chance of getting a group to ult against.
McCree is also useless, but I don't know that any changes can make him useful, and that's not going to change the fact that people keep picking him.
@AppleCider Typically both teams don't get the flag at the same time. Most of the time when I see that happen it means both teams have inadequate defenses and someone else will score a go ahead point eventually. Or it means someone was losing and they shifted to a more offensive strategy in order to tie it and the trade off comes with the cost of losing another flag.