Well, but: if actually Wii U is not able to running "at its best" the Frostbite engine, I think that we can say farewell to the UE4.
Is that a big problem? I don't know, probably yes, if UE4 will be use as much as UE3 in the next generation...
No.
Ok.
Let me try this again.
Let's say you have system X and system Y. Then you make game engine A.
You have engine A running at 100% optimization on system Y (this pretty much never happens, by the way, but for the sake of argument...).
Then let's say system X comes along and you try and put engine A on it. You can't just plop the code into the memory and expect it to run like it would on system Y.
You need to rework it.
This is what they are doing right now. This is what Nintendo is striving for. They want to make the system optimized for popular engines, and, with non final hardware they are working towards that goal.
They could very well get it running perfectly where EA or whoever wants it to. They could not.
Either way, we can't say for sure based on what we know right now.