The title says it all. What would you have done differently if you could have designed any of the consoles? 

For me, the PS4, since that's all I currently have now. I would have; 

• Made the PSU smaller or external to allow for an even smaller console and put in a bigger cooling fan.
• And from above, would have been able to clock the CPU/GPU at 2Ghz/1Ghz respectively.
• Would have gone with 12GB of Ram, locking off 4GB exclusively for the OS and leaving 8GB for apps as opposed to the 3GB OS 5GB app configuration used now.
• Used a sata 6 interface for the HDD instead of the sata 2 used currently so people installing an SSD can take full advantage of 500MB+ transfer speeds as opposed to the 150MB-200MB peak now which would make the system even faster and loading times considerably less.
• would have made the touch pad on the controller a capacitive touch display and of the exact same size, so it could pass for a touchscreen keyboard in addition to a track pad. 
• Would have made features like PSshareplay and PSnow day one features. 
• Would have put a bigger battery in the controller. 

Survey Corps brother, here's my answer:

PS4: made the sticks on the controller like the DS3 sticks and turned off the damn LED when not needed, would have also removed the duct tape-magnet LED strip from the console and included compatibility with legacy video cables

WiiU: sell game bundles with a Pro Controller just like the Wiimote bundles, made it play video files and BluRays/DVDs. Perhaps used Wacom technology and higher resolution on the Gamepad if financially viable.

Made sure the rubber on the DS4 analog sticks was of a decent quality with good durability. Both of my controllers are getting rub wear and tear on the analog sticks. I'm going to have to resort to those fugly analog stick caps before long.

I dunno about the RAM. Seems like going from 512MB RAM to 8GB is about a 15x increase. Even the available RAM of 5GB is 10x the available RAM for games on the last gen machines.

Sony is better off having the bill of materials come in at below the MSRP for the console, that way they can get to profitability on hardware much quicker.

Little things mostly for PS4. I would make the LED be able to turn off. I would have the old audio cable ports. I would also make the HDD 3.5 instead of 2.5 so it's easier and less expensive to replace. Oh yes and I probably wouldn't have had the touchpad at all as well as made the sticks not rub off as easily (one of mine has gone off on a tiny spot) and made them just recess in the middle as opposed to the lip they have now.

For the Wii U I would've gone for a non-custom design for the CPU/GPU. Heck, even the same CPU/GPU that's one the Xbox One. Even a slower and less powerful version of that one would've been ok. That should've been enough for software emulation of Wii titles and would've been cheaper to produce. Also, 4GB of RAM with a wider interface.

Oh, and a smaller screen for the Gamepad, maybe something that was being mass produced for big smartphones.

Funny thing is that of the 3 current gen consoles the WiiU has the biggest memory bus interface. Though it uses the cheapest slowest clocked RAM. 

Ah, yes, worded that wrong. I meant a higher memory bandwidth for the main RAM. The eDRAM is pretty cool as it is.

For both Ps4 and Xbox One
-Optional Mouse/Keyboard support for FPS games.
For Xbox One:
-No Kinect and Moar Power, same price as the Ps4. Since Sony has financial issues now, I would have played the loss leader card again.
For WiiU:
I wouldn't have made it in the fist place.
If they wanted to cater PS/XB audience I would have made a console similar to Ps4 or XB, a just a little cheaper and less powerfull. Plus Wii/GC HD retro-compatibility via emulation.
If they wanted to cater the former Wii audience I would have made a cheaper and simple console (199$ price tag). No exotic controller. As optional I would have made a cheaper DS (original) version to be used as a controller (like a 2DS). 4 player-support.
I would have pushed digital distribution with more competitive prices and uncoventional forms of distributions. Also I would have started the architecture unification process they are likely doing today.

Wii U: Make it a PS4 with Nintendo exclusives instead of PS exclusives, name it Nintendo Fusion or somehin', make sure that it doesn't have any gimmicky things that would make most people roll their eyes and buy the competition instead.

I'd keep it at $400 on launch so the only thing I'd change is removing the PSU to an external to allow for greater cooling and a even smaller (shorter) console, which also would have allowed for greater upclocking.