The path that Wesker flies around the screen is semi-random. It consists of attacks that always come at the same angle, attacks that always head for certain areas of the screen, and attacks that lock onto your character. Because of this, some hits will hit you and some will whiff.
(Fun fact, if you raw tag or alpha counter during Maximum Wesker, these attacks that lock on lose their target and Wesker will usually fly harmlessly towards the top of the screen. This is also why Wesker derps if you use Maximum Wesker against Galactus).
Most of the time he will get you with the first hit, you will block it, and then autoblock will block the rest of it for you.
(If you don’t know, autoblock is the property that if you are already in blockstun when another attack hits you, you will automatically block that second attack as well. Even if you have your stick in neutral and even if it crossed you up. However, you still have to block high/low.)
Sometimes the first hit will whiff. The second hit will come from the other side and cross you up.
Sometimes you will block the first hit, but somewhere in the super he whiffs enough hits that you leave blockstun and autoblock is no longer going to help you block the rest of the super, and you may need to block a crossup/not a crossup again.
(You can somewhat prevent this from happening by push blocking every single hit - pushblock extends your blockstun a bit. Also, when done correctly this completely negates the chip damage from Maximum Wesker. Of course, when done wrong you will throw out an H and get hit by it.)
Just keep playing against Wesker. Eventually you will develop a sense for it.