How can I compare two different neural networks, from a theorical point of view?
Essentially, no.  The only way to know which neural network is going to give you better accuracy is to try them on a realistic data set.  The theory we have is not well-enough developed to allow us to reliably predict which will do better on a particular data set.



A secondary remark.  When you remark "other programs might interfere", that's not correct.  Even if other programs are running (on a multi-tasking machine), they won't affect the accuracy.  They might take the process of running or training the neural network on your data set take longer, but they won't affect the results.