Flags and the bonuses they provide are the incentive to control territory. It creates goals to strive for, it forces teamwork and creates hotspot territory wars.
Play a few games of Fortress: Notice how the dearth of flags tends to center action in one spot for the most part... the main creep lanes. In every other mode, the large variety of flags give you a reason to walk around and do stuff, and a bigger incentive to stay in your lane... or at least invest in a flag lock if you intend to leave it.
Crucible is, yet again, odd man out. All its flags are off by themselves, and especially the lower two flags are a death sentence to send demigods to, sometimes.