This is just me spewing theory, since I don't play Raijin, but from watching gameplay videos of vDalphanate (the only competitive Raiden main as of right now) i feel Raijin still struggles against most characters and especially against zoners. Watch the first match against Cetrion in that 2+ hours of (mostly) Raijin KL play YouTube video from vDalphanate and you'll see what i mean. He got thoroughly destroyed.
In my opinion Thunder Wave is still the superior variation overall. The teleport is just too powerful for anything Raijin has to overcome. With the teleport, Thunder Wave Raiden cannot be cornered and he can almost instantly close the distance to any opponent. Those two things alone are enough to make Thunder Wave the superior variation. He can also play mind games with far, close, in place, and Amplified teleports.
In addition, Thunder Wave has better combo potential. Storm Cell is easier to follow-up with pretty much anything for combo extension, while with Raijin you are limited to F2, F4, or dash forward into an extension. In other words, the execution is higher with Raijin which could lead to higher rate of dropping combos, which in turns leads to less damage, loss of turn, and potential punishment from the opponent. Plus, with Raijin you always have to have Quick Charge activated to be able to do bigger combos, which is yet another thing to worry about during a match.
Another downside to Raijin is that he always has to have Quick Charge active to play his best game. That means you have to find ways to activate it safely and in many cases that can result in loss opportunity for incurring damage. For example, i saw several times in vDalphanate's video above how he did B1 into Quick Charge when he could have followed-up with 2 into combo or block string for chip damage. Plus, Quick Charge expires in 15 seconds, so you have to constantly manage that thing.
On the plus side, Raijin with QC active does have access to Discharge, which is great for interrupting the gameplan of rush down characters. Also, he has a really good full screen Anti Air with Summon Lightning. Those two things are just not enough to put him over Thunder Wave though.
