Playing both, I'd say this matchup depends mostly on the Valk player.
In terms of movement Valk > Makoto and given Makoto's hard time at getting in it's better to play this matchup passive until you force Valk to pick a risky option, once you get in always end for oki and consequently stay on his arse the whole time, he has no solid reversals untile he gets his 50% (though I have yet to see a Valk player using a CA, most of the times it's spent for RC/or combo ender with his KoF super), and your 2A > his 2A. Cornered Valk = hopeless Valk
Valk's blockstrings can be easily IB'ed however keep in mind that 5B from almost max range can be staggered and they will do it knowing Makoto has no way to punish these pokes from that distance (unless you IB>parry), specially since Valk's blockstrings tend to push him away real quick. His 6C will dodge your lows so even if it's slow they can still catch you off guard. If they're using it at the end of a blockstring you can IB the previous hit > parry overhead and make them afraid of using it. Don't just block the overhead though, it's freaking +6 on block, and be aware that he can kara-wolf cancel the move as well: if your parry "whiffs" because of that and he's getting in with the wolf fakeout get ready to block or DP (depending on the timing/distance).
If Valk resets his pressure with a fakeout (4D/7D) get ready to block a [w]j.B and be ready for mixup as he lands (it's either [w]5A>[w]5B > crossup [w]j.B, or the command grab). Wolf mode pressure can be slight of a pain in the butt you'll have to patiently block (not easy to IB wolf 5A) and wait until he resets, then parry as he gets back in. He could also try to get away with his wolf 236A/B (kinda like Bison does with the psycho crusher), parry that shit. But if he uses 7D he'll end up falling diagonally there's enough time to use 6A/DP. Just be aware that after his shoulder special he will wolf cancel away (if you IB'd, that is. If you just blocked he might keep pressuring with [h]2A but you can IB all the stuff that comes after).
If Valk hitconfirms a poke from max/medium range he'll go for the shoulder special unless he's within range for 3C > walk 2B. If he ends the combo with 236A (and he still doesn't have 50% meter) he can still bait your reversal DP (however most Valk's will be eager to keep pressuring or wolf cancel).
Also, watch the hell out for his 2C. Bait it, use j.2C/double jump whatever just make that move whiff because even if it trades it's in his favor.
As for air vs air, his j.C is good but Makoto's j.B has a good vertical hitbox (and it's faster) if you see Valk approaching from fullscreen with his wolf cancel'd dash don't be afraid to jump and j.B. His human form j.B is a pretty good antiair but doesn't seem to have a huge vertical hitbox (but it hits behind as well, so be careful for that), meaning that if you're above him you're almost safe since his only option it's his j.214B. If you happen to block his j.B in the air be ready for j.214B (if they attempt that it's a free air IB for you).
Overall this is a matchup that requires a little patience, though you can't let the Valk player take the initiative it's not easy to get in, so basically it all boils down to patiently wait/create the opportunity to turn the momentum and RTSD. Though remember the more the game drags, the more it turns in Valk's favour, he can gain meter as fast as Makoto and move/fool around as he likes. It may also occur a situation where Valk is just sitting around and just pokin and playing footsies until he has 50% meter for easy hitconfirm > RC combos. When things become like that just be careful and IB/parry as much as possible. Once you get a knockdown it's your turn to make him feel sorry for not having chosen to be aggressive right from the start.