I am going to echo other people have said and agree that Xenogears is not really a deconstruction on par with something like Neon Genesis Evangelion. The only two elements Gears really does differently from most RPGs of it's time is portraying Fei in a more human light by making him anything but ideal, and making the villains far more sympathetic than is usually common for RPGs. Of anything, Xenogears is more of a Reconstruction of the Giant Robot genre as Fei has more in common with characters like Amuro Rei but like Shinji, he is given very good justification for not wanting to pilot a giant robot beyond informed values like Amuro.

The only real deconstruction I could see for the game is maybe being a deconstruction of the Amnesia Plot, unlike most recipients of amnesia, Fei actually get's his in a bit more realistic way (psychological trauma) whereas most cases of amnesia in the series is due to magic or getting knocked on the head but then miraculously cure themselves with no real treatment. Instead Fei lost his memories of his own volition to save himself from the trauma and that is actually a real phenomena in Psychology where people can consciously suppress their memories and personalities. whereas head-trauma caused amnesia tends to make the character suffer from brain-damage function which RPGs and media rarely go into cause it's jut a plot device. Even then it is more of real take on the subject as opposed to a direct deconstruction.

I think the comparison with Eva is largely due to both games being about reluctant heroes with psychological trauma, piloting god-like Giant Robots, and trying to stop an ancient conspiracy with heavy handed religious concepts. The issue here comes down to intention, and that is why one if a deconstruction while the other isn't. Eva deconstructs the giant robot genre by showing you what a more disturbing but probably true-to-life take on the whole "boy and his daddy's robot" plot whereas Gear plays it straight and just happens to exist in a world that falls into less idealistic territory than the genre is known for.