Makoto is really good. If you can't do her jump-cancel parry combos then just try to keep the pressure on. Her damage is average without doing the jcp, but with them it's very good.
Don't forget her fireball close-range. It keeps people in place setting up mixups and removes a primer as well.
If you have 50 percent meter and the opponent does anything, from anywhere, feel free to use her super. In fact, even if they aren't doing anything you can use it if you want to.
Other than that, she's pretty straightforward IMO.
Extending upon this, when midscreen, using the parry loop, make sure to finish the loops with either 6C --> 214A~A or 2D(2). I prefer 2D(2) because it's much better Oki, but sometimes muscles act on their own so it's good to know the other option. Good thing to remember as well, 6A is the only viable JC-able move on block and therefore Parry Cancellable for more pressure.
If you have a fireball set up on the opponent, I would much rather leave the fireball on them and continue pressuring.
Big Bang Smash is amazing, abuse it. Forget Particle Upper, that move is bad compared to Big Bang Smash. BBS does more damage in later combos, btw. Makoto builds heat like Ragna, but I still prefer to save Meter for BBS punishes or RC'd blockstrings rather than in combos.
Makoto's approach is bad, you're going to have to dance all over the place and bait parry's before you can actually put the hurt on. If you run into someone air-to-air, j.B is very fast and high priority with a ton of hitstun.
Her best combos are going to take a bit of practice since the timing is wierd. The best one that I know of that isn't on the front page of the combos thread on Dustloop for some reason is:
(Off of 5B>5CC or 6B~C) 5D, 66, 2C, 2D, j.D (must be underneath opponent when hitting), 214B~D, 214C(slight delay)~D, 236A~D, 6A, air combo.
(Off of forward throw) 214A~A, 6A, above combo.
(Off of back throw) 214A~C~D(2), above combo.
Against Lambda and Carl the 236A~D must be level 2.