Both are two different stories written in different times. Both focus on different themes. However, the best way to compare these stories would be to understand them both as socio-political critiques. Both critiques do their works in a different manner.
For instance, for pointing out the shortcomings of a society Gulliver travels to new and strange lands and meet new people such as “Lilliputians” and “Brobdingnagians” and points out the shortcomings of their societies.
Orwell uses a world of Big Brother, where he shows the worst possible future outcomes due to bad political administration, goes out of control and manipulates the people through use of hate and fear.
Hence, we can say that both these stories criticize politics and society, nevertheless each one does this by using its unique and effective method.