Haven't seen many good Makoto's yet, but this matchup really doesn't seem all that hard. Makoto has trouble getting to enemies, and who's one of the best characters and being evasive?
j.B beats pretty much anything she's got as an Anti Air, and her options in the air seem quite poor. Summoning clouds, IAD j.B and
2D/6D 'keep away wall', should stop her from touching you.
Even in the event that she gets close to her, her mixup seems quite poor and I've noticed you can use 5A/2A to counter a suprising number of her attacks.