The worst part about GATE is that because it is somewhat popular, now if anyone ever tries to do something similar to it, people will claim its just a rip off.
But to move onto your main point, there are a few ways GATE could be improved, in both the controversial issues and in the general writing. The controversial issue, ie nationalism, has two solutions:
1. Real world politics are involved but no single nation has control over access to the fantasy world.
2. Focus entirely on the contrast of fantasy vs. modernity and ignore any real world consequences.
Now, if you want to do #2 you have two options, the first of which is to make is a Band of Brothers type story just focusing on the lives of a single military unit, but this has issues with how to make it last more than one season. The other option is to make the main POV a member of the fantasy setting, but it undermines the entire point of GATE, so I don't think it is a good idea either, so real world politics wins.
Now, something I need to point out is when I say real world politics are involved, I don't mean they should be the focus, nor do I mean political issues that exist independent of the fantasy world should be involved. Rather, I mean there should be multiple nations in the fantasy world allying themselves with the various real world countries involved. Which brings me to my first big difference with the premise of GATE: there should be more than one portal. Ideally, there should be not too many so that travel between the worlds can't be controlled, but enough so that no single country has a monopoly on them. Ideally, there would be 4-5, with most of them in major countries and then maybe one or two that end up in poorer nations that can result in problems for the second season. Also, if you don't want the influence of the fantasy on reality to be the focus in the first few seasons, don't put any gates in the middle of major cities. Put them in suburbs, so that there is still conflict.