Arduino - manually ceate objects (e.g. WiFi library)
I am not sure, if it would save enought memory to be worth the problems (it is just few bytes, buffers are created anyway), but lets say so.
Then you need modify the library to not creating the object, as it is allocated statically and cannot be removed later (and reclaim its memory). To protect all other projects it would be probably best to use special #define to disable it only in memory critical projects - so the Wire.h should contain something like

#ifndef EXCLUDE_WIRE
extern TwoWire Wire;
#endif


and your program (critical.ino) should start with

#define EXCLUDE_WIRE
#include &lt;Wire.h&gt;


and then somewhere in loop / other function use 

TwoWire Wire;


as local variable. If you need to call other functions with it, then you have to send its address as a parameter.

Anyway you will not save nearly any memory, as nearly all variables in TwoWire ((and namely buffers) are static and so class variables and so are common for all instacies of TwoWire and allocated automatically if there is (possibly used) any instance of TwoWire anywhere in your program.

So it would be better to create your own library to use the same functionality, but make sure, that all such variables are instance variables and properly created and released at the right time. This would also allowe for changing the buffer sizes, if needed. 

As it is under LGPL 2.0+ you are legally allowed to do that (provided you fullfill all licence conditions).