Actually, I think that in native apps, the A9X might be faster than i5 native apps. If you compare them equally. Looking at Geekbench, which is one of those apps designed to be native, you can see how the A9X is as fast, and in some cases faster, than the i3/i5 processors. It all depends on the software guys.
There is no such thing as a native i5 application. There can never be a benchmark that treats an x86 and ARM CPU the same. There are instruction sets that ARM processors cannot compute, but certain x86 processors can. All of these "universal benchmark" applications cannot use these instruction commands, as the ARM CPU cannot handle them. Geekbench is an extremely basic benchmark and should not ever be considered a credible source.
A true benchmark would be getting an i5 to run on iOS or get the A9x to run x86 programs. Neither will happen, so neither should be compared.
Until there is a benchmark that is universal and supports proper x86/64 instructions, we will never know the true speed comparison. iOS has an insanely low overhead compared to Mac OS X or Windows, and I can guarantee that the A9x would not be able to run either of those operating systems efficiently.
Aka, no point in comparing them to each other. There will never be a proper, fair way to evaluate either CPU without constraining it.