Suwako is a big problem right now! Sam went on a crazy win streak after switching to Suwako lasers, and it's mostly because the lasers help Suwako get in. I think part of the reason is that I was playing low tier garbage, but it's a good analysis to find out exactly what is winning and why.
I think it goes without saying that Suwako is about as threatening as Sakuya if she gets you blocking. Suwako doesn't have the crazy mixups that Sakuya does, but her stuff is airtight, hard to escape, and she does way more damage than Sakuya. We all know this, and if you're threatened by it, use more bombs or raiments.
Suwako's bullet options come in the form of various cover bullets and her bullet punisher, j6c (or 66c). If Suwako is in the air, she can throw cover, then attempt a punish with j6c. Unfortunately, j6c is a bit slow, so it relies on density to reach its target. This has some problems. If you see Suwako throw cover, you can fairly safely throw any bullet (ideally a bullet, not a laser) that beats j6c and be at a large advantage, since Suwako must graze. After messing around a bit in vs. CPU, I found that the following bullets consistently win:
Reimu: Default 214 barrier, alt 236 Youkai Buster
Marisa: 6c laser, anything similarly dense (eg. Narrow Spark). Marisa has few options and has problems in this matchup.
Sakuya: All C bullets; d.236 Seven Star Sword. Sakuya is basically uncontestable at any range by Suwako.
Alice: C doll bullets are safe and indirectly win, since Suwako j6c will not hit them, allowing Alice a free doll setup.
Patchouli: alt.236 Summer Flame, d.214 Autumn Edge, alt.214 Autumn Wind. 5c also indirectly wins, since it goes around j6c. Patchouli has many, many options here. Summer Red technically also wins, but will only hit if Suwako is very low to the ground.
Youmu: Nothing other than her d.236 reflector. Youmu has a lot of problems in this matchup.
Remilia: alt.214 Demon's Dinner Fork, alt.214 Stigmanizer. I highly recommend switching to one of these alt cards against Suwako. Remi's vs. Suwako is harder than most, even with these options. alt.623 Rocket Kick Upper also works, but is an unreliable combo tool, not a danmaku punisher.
Yuyuko: d.214 Ghostly Butterfly goes around Suwako's danmaku. d.236 lasers also work, but they're lasers and not a good choice. 6c is also very effective, but slow to execute. d.421 penetrates, but only works in certain screen positions and is not very good against j6c. 5c is effective if cancelled early.
Yukari: C bullets. Yukari has few other fullscreen dense bullet options, but she doesn't need them. She can just 6c on reaction to any Suwako cover and completely rule the screen.
Suika: Technically almost anything but only Oni Spirit Bomb is any good. 6b does not work reliably. Oni Spirit Bomb is absolutely mandatory in this matchup.
Reisen: alt.214 Eyesight Cleaning is the only air-usable skill that works for sure. Ripple Laser might, but it's hard to test, oddly enough. Reisen 5c can still be threatening, even though it can't penetrate.
Komachi: Only alt.236 Scythe of the Reaper and only at certain distances, which Suwako will almost certainly avoid. Alt 214 blue spirits can get on the screen when normal 214 cannot, so it might be good.
Iku: Alt. 214 Dragon God's Lightning Flash is her only real option. Whiskers of the Dragon God also work, and Dragon God's Wrath can provide protection in case Suwako dashes in. Lightning Flash is mandatory in this matchup.
Tenshi: While 6b doesn't seem to work, almost all of Tenshi's other bullets do. Tenshi absolutely rules this matchup.
Sanae: No normal danmaku works (well, 6c does), so she must use assists to prevent Suwako rushing down instead of trying to beat danmaku directly.
Cirno: 6c only. alt.236 lasers might; could change this matchup considerably if they did.
China: 5c/ground 2c only. This is a problem due to angular geometry; as China you should probably try to stay level with Suwako or directly below her as much as possible to prevent danmaku pressure.
Based on the above information, we can safely group characters into a few tiers:
Completely shut down Suwako's danmaku: Patchouli, Sakuya, Yukari, Iku (with DGLF) Tenshi, Utsuho
Strong against Suwako's danmaku: Reimu, Alice, Yuyuko
Have options against Suwako's danmaku: Remilia (with alt.214), Suika (with OSB), Reisen, Komachi (with SotR), Sanae (with an alt assist)
Have problems agaisnt Suwako's danmaku: Marisa, Youmu, Cirno (possibly), China
Of course, danmaku isn't the whole matchup. The rest of it is Suwako's melee approaches: 66b/6a/j8a (tree) j6a and j2a. All of these have one thing in common; they are extremely unsafe on whiff. Any character with strong punishment options (via bullets mainly) can turn situations with these moves into her favor by baiting a whiffed attack. If you have poor options against her danmaku you will spend most of the round either rushing down or getting rushed down, which will lead into the next section. This section mostly covers characters that can deal with her danmaku, forcing Suwako to change tactics.
A blocked tree or dive is not a big problem for most characters. Suwako must cancel after the tree, and almost anything she does loses to many startup graze attacks. In particular, Yukari 623b wheel absolutely crushes Suwako here; there's nothing she can do except get wrecked. Tenshi default 623 also absolutely ruins Suwako here and there's nothing Suwako can do. Sakuya default 623... again, anyone with a forward-moving startup graze attack, preferably with a disjointed hitbox, has a strong advantage here. Youmu can actually fight out of this situation with her 623c if she dashes forward, but Suwako can cancel the tree into a melee special and possibly win.
j6a is just a big problem for everyone. The best situation possible is simply to beat her danmaku and deny her the approach angle with anti-air bullet cover or anti-air melee. The other option is baiting it. Of all Suwako's tools, j6a is the most like another character's midscreen game. Predict it and counter and the matchup will be a lot easier. Once blocked, there's no safe escape since you don't know exactly when Suwako will cancel or what she will cancel into. If you have one of the startup graze options mentioned above, they will probably work. Otherwise, you'll have to guess. Bombing/DPing is highly advised.
Being put on the defensive against Suwako is very hard. Once she gets in on you, it's hard to escape. The first thing to remember is midscreen, she must do some melee into 5b, airdash forward, j5a into a mixup. She can 5b into another airdash or land and attempt a reset.
If you predict a reset, you want to DP there. DPs with lots of invincibility (including bombs) also can work for both options, though you must react quickly or Suwako can dash cancel her 5b and escape.
If you predict a bullet, any startup graze special works. Lacking that, you will want to border escape the j5a. If you're not in the corner, you have the option of border backdashing. This can potentially force a whiff, but if Suwako cancels her bullets into more bullets (in other words, predicting a border backdash) you are totally fucked. Bordering straight up is a better solution.
Note for Suwako: On block, j6c is somewhat risky since the airdash forward is difficult if improperly timed and 5b > j6c is not airtight on block. IMHO it is better to omit 6c unless you are sure the opponent won't border up. If the opponent borders 5b, you can airdash j5a to punish. In fact, since 5b deals a full spirit orb, you're probably better off not doing 6c at all unless the opponent has only one orb left. Even then, your opponent will probably border if he's smart since a blocked 6c means guardcrush into 2k and a bluering, a j5a hitting aerial means 1k and a wakeup mixup.
Don't airtech against Suwako. Ground mixups are way easier to deal with as Suwako's oki is bad. If you have a fairly long ground tech or an unpredictable one, Suwako has no way of getting a reset. Some characters, like Yuyuko, are in a bit of trouble in either case but you are still better off playing the guessing game on the ground rather than trying to fight a tech punish in the air. Suwako has a lot of trouble chasing ground techs, and if she guesses wrong you are in neutral again. Air teching will never give you this good of a situation!
Going off of what we learned above, in a midscreen situation, Suwako's options are fish with trees, j6a, or j2a, or deploy danmaku. If you have options such as Yukari 6c or Tenshi 2c that beat all of these, just employ those if you are in a neutral situation.
Suwako wants to take to the air in a midscreen situation and will do almost no fighting on the ground. Prepare danmaku responses accordingly. Don't throw low-density danmaku in this matchup; almost all of Suwako's danmaku is medium density and will beat it. This means stuff like Yuyuko B butterflies and all Iku bullets other than alt skillcards. Some low density danmaku such as Yuyuko's 214 butterflies are obviously good, but in general you want to stick to high-density danmaku until you have advantage. Once you're at advantage, play your normal gameplan.
If you don't have high density danmaku or setup danmaku such as Yuyu d.214, you will need to play a passive graze game and bait j6a or trees. If Suwako whiffs, take advantage immediately and go for the kill. If you have alt skillcards that win the matchup, throw danmaku whenever it is safe in order to build card gauge.
Once Suwako is on offense, if you have a special with startup graze, use it to break out of her pressure before it starts. If you block a j5a or a ground 5a, you are hosed without a border escape, bomb, or DP. Save your bombs and reversal spellcards for when Suwako starts her offense.
As soon as you get a little advantage, capitalize and lock her down. In general, in "even" danmaku matchups (eg. Remi, Suika, Reisen, Komachi), you will get more opportunities than Suwako because Suwako has less mobility. If you lose the danmaku matchup, you will have problems. Suwako has trouble escaping most things because she has poor mobility, so you should keep her locked down as strongly as possible.
Be aware of Suwako's lily when on offense. Avoid "low" attacks that cannot hit the lily and force Suwako into blocking high by using frequent overheads. A whiffed low is extremely painful. On the other hand, lows that can hit the lily, such as China 2a or Youmu 3a are quite good (unfortunately Youmu has no good overhead T.T).