Whether she's low tier or mid tier is debatable (v-ryu, Flash, and myself think she's mid...not that I'm comparing myself to those two), but she's definitely not bottom of the barrel. Her mixup game is too good and she does too much stun/damage off those mixups to be at the bottom of the bottom.
IMHO, her only real big problem at this point is getting in a position to take advantage of those mixups. Every option she has to close space has too much risk associated with it.
Dash in? Pretty easy to throw out random low pokes into an option select to discourage that.
IA tsuguri will tag a lot of those pokes, but if they're just blocking she'll be a bit closer, but at negative frames.
Hayates are pretty safe on block *if* you space them right (which I don't, more often than not), but ex hayate is -4 no matter what you do. Again, though, pokes into option selects tag random hayates.
Another issue to address is her defense. Possibly. But like I've said before, her lack of defensive options never bothered me much, but I've played Viper for a year and her defense is similarly shitty, so maybe I'm just used to it.
But yeah, all that said, I think it's still too soon to make any adjustments. There are things I thought about Makoto a month ago that I was completely wrong about, and I'm sure there are things I think about her now that I'll end up being wrong about next month.
You on some crack