Wakeup defense is very hard, so try to not get too discouraged. I think the #1 thing that helps with wakeup defense is knowing what your opponent's options are midscreen. Not that many wakeup situations are true 50-50s where your opponent can meaty throw or strike. I would hazard that most midscreen wakeup situations are not subject to meaty throws. Many are, but I feel like that's not the majority case.
Unfortunately, knowing what your opponent's options are is very character-specific, aka requires broad game knowledge and lab time. For example, Zangief can put you in a true 50-50 after heavy SPD or EX SPD, but not light or medium SPD. That's on you to know because they all look similar, only having slight variations in the altitude of the SPD and slight variations in spacing post-attack. Also, if you get DP'd out of the air vs on the ground, your opponent has more time to get close to you because you're falling from much higher up in the air, for example. So there are also situational things like that. If you don't know whether your opponent has the frames to walkup/dashup meaty throw, then I suggest hitting buttons and see if you eat their attack. To me, it's worth risking the damage to get the knowledge.
You can also go to practice mode and re-create the sequence. Choose the character you went against, set the CPU dummy to do a wakeup 3F, then do the move and try to meaty, dash-in meaty, or whatever was happening to you in the match.
Another thing that helps a lot is to recognize tick throw situations, and this is usually point-blank crouch jab, from my experience (certainly varies). It's whatever has minimal pushback and keeps you in throw range. Get used to processing whether the meaty attack leaves you in throw range, and act accordingly. If you are in throw range, consider late tech. If not, keep blocking and watch for a walkup grab.
Here are my very quick, off-the-top wakeup option rankings -
1. block and let the pushback do the work for you. Possibly eat a throw, but it's better than getting combo'd.
2. late tech if they are in throw range (which again, is not as often as you might think).
3. delayed jab/whatever your fastest move is (although, vulnerable to shimmy just like late tech is)
4. reversal DP, but this is situational. It's best to do it when you can afford to eat the punish, or earlier in the match so that it will mess with your opponent's head more. Also, know the risk-reward. I'm much more likely to wakeup DP or wakeup super if it will win me the round. Especially if it's 0-0 or I'm up a round and I can afford to lose a round.
5. mash your fastest normal
The problem with neutral jumping is that if your opponent has good wakeup pressure, their attack will recover in time to anti air you (AA jab generally works against a point blank NJ), which puts you right back into the oki blender. So you should generally only do this if you're reading command grab. I'll do it when I'm trying to bait Giefs into wakeup super, for example.
The problem with backdashing is that if you get hit, it's a counterhit guaranteed, which means a crush counter if your opponent hits you with a CC normal. I feel like a wakeup 3F/4F is better than backdashing because you at least give yourself the chance to hit them if their timing is off. However, in the corner, the payoff of a backdash is bigger than neutral jumping because, since you have nowhere to go, it puts you at point blank range so you can punish or at least apply your own pressure and fight out of the corner. I see people do this mostly against R. Mikas.
>so what are you supposed to do against someone like birdie or
>alex with great oki buttons and command throws? i feel like i
>can't 3f because i'll get crush countered. i can't block
>because i'll get command thrown. jumping gets me tagged out
>of the air for another reset. backdashing seems like the best
>bet but it's still a 50/50 situation. even against characters
>without command throws most wakeup situations feel like the
>above. i'm guessing (especially in the first 2 rounds) and
>when i guess wrong i eat 35% damage and a gang of stun. are
>you supposed to just take the throws? is this why throw
>looping was nerfed?
I say this with zero sarcasm - step 1 is don't get knocked down. If you're at close spacing and you're afraid to throw out a button, then you should walk back, jump back, whatever (backdash is okay at longer distances) to get yourself out of the situation. Reset the spacing so you can try to start your own offense. If you choose to stand in there and hit a button, you're rolling the dice of possibly getting counterhit, knocked down, etc. You could gain from the situation, but why not reset the spacing and go for something with higher probability than 50-50? That's my outlook on it.
And to answer your last two questions, yes, you're generally better off just taking the throw, and yes, this is why throw loops were nerfed. So even in the corner, most forward throw loops are gone.