I'd be interested to see some matches of you two playing if there are any? No offence but it does sound like you are playing the matchup not entirely correct. If Wafflez was whiff punishing a lot of your d4s, I have to say that just comes down to a bad footsie game on your behalf as Sonya's d4 is a lot more superior than smokes b2 imo. It's 3 frames quicker, it has a lot more range, incredible mix ups with it, and it can even avoid the smoke bomb. Smokes D4 into any string or throw can be armoured out of. There is a 3 frame gap to interrupt the b2 after D4 on hit. Yes the armour can be baited but I thought it was worth mentioning. With the combination of good spacing of d4, ex cartwheel and a dive kick that has priority over pretty much everything, I can't see the footsie game being that much of a struggle for sonya. After Sonya's cartwheel on block there is a huge guessing game and it heavily favours sonya in my opinion. Some things worth mentioning.. Sonya can dive kick any string follow up after a d3 on hit due to it being 5 frames or simply just d1 linked into a special such as d1 cartwheel, or she can simply armour of course which is always a major threat. That's if smoke can manage to hit you with a d3. Although under used, sonyas standing 4 is a superb counter poking tool as it's 10 frames and hits mid. I especially like it for punishing D1s. I also like Sonya's standing 1 for counter poking with which is a very good punisher for d1 smoke bomb. However, if you block a d3 or d1 and they go for another poke, they will beat your standing 1, which is why I like standing 4 for counter poking so that stuff won't happen as it's a mid. Smoke has a very hard time dealing with Sonya's d1 linked into specials as he doesn't have a solid option to interrupt it, as opposed to a character such as johnny cage who can get a combo from b3 or f3. I think mix ups such as d1 ms overhead and d1 ms f1 are a very good option as Smoke has a very hard time punishing it. Smoke always has to keep his pressure short as he is always at risk of getting hit by that 5 frame dive kick, or ex cartwheel, or 7 frame standing 1 or d1 linked into special which he can not even punish well if read. Sonya is one of the best characters for punishing smokes 214 string. If sonya is crouch blocking and smoke attempts this string, it is very easily punished with standing 1 or dive kick as the 2 and the 1 both whiff over her head. Sonya is also the character with the best punish for a smoke bomb on block, being able to punish it for an incredible 40% meterless midscreen with a reset. I believe I have witnessed waffles doing crossover jump kicks a lot in this match up which can be punished very nicely with ex cartwheel on reaction into ms b2 b21f2 112 ms for a tasty combo of around 30%. To be honest you should not be getting your wake up cartwheel whiff punished often. You need to be more careful with it and not risk it when smoke is a good distance away or yes it can get punished easily.
When sonya manages to get smoke in the corner which she will, it's pretty much game over.