Riot has always rewarded players for landing skill-shots. For example they changed Ahri to be more rewarding for landing her stuff. Like you said the AP scaling makes absolutely no sense. There's nothing wrong with scaling a magic damage ability with AD such as Shyvana's burnout.
There is an idea to make the Q mark the target and she gets more move speed going towards the target, which is similar to Nidalee. So it either must have a slow or move speed.
You're right about she should get something more while using her tunnels. When I watched a video where she uses a tunnel and Janna knocks her up my mind just did a double take. It didn't make any sense. Some people complain that it will make it harder to deal with her, but she should get something. Perhaps you can still damage her but she can't be disabled. So either: can't be disabled, or untargetable while using tunnels. Perhaps she should even move a little faster than they have her doing now too.
There does seem to be a bug on the PBE where you can see all the tunnels of an enemy Rek'Sai after a certain amount of time, which makes it that even putting them in bushes doesn't do anything. I'm sure they are fixing this.
One last bit I'd like to add as my personal touch. Champs like this that need to be in melee range usually get some sort of reward for engaging and staying on a target other than just simply killing the target. I'm speaking of champs like Tryndamere, Scarner, Shyvana and Xin Zhao. All melee characters that have a similar mechanic. That being that auto-attacking reduces the cooldown of abilities. (Yes I know Xin needs his Q but yes it's the same mechanic.) All of them have the same idea in mind, which is sticking to a target. I think Rek'Sai should have something similar. I know the idea of having her ultimate be reduced by engaging in combat is too much to ask so I won't. Her Q and W are on such a low cooldown that it would be silly to ask for that either. What I would ask for is that for every hit of Queen's Wrath (Her unburrowed mode Q) her E for both Furious Bite and Tunnel the cooldown is reduced. It may need tweeking, but let's say 0.5 seconds, and 1 second on champions. Should it also reduce the timer for knocking up targets? Nah that would probably be asking for too much. I'm sure they'll do an 8 second timer by the end of it anyway.
All of these things need to be tested, but that's why she's on the PBE right now.