Do you have the Platinum Edition, the Renewal of Evangelion, or the Blu-ray Box? Because believe it or not, none of those are the original version of the series.
The most commonly available version of the series is the edited version, which introduces changes to the animation, sound effects, and music. In my opinion, these changes fail to punctuate key moments of the story as effectively as the original version. Some of the changes also create continuity breaks, and the color palette has been tinted blue. See Original vs. Edited for a closer look at the differences.
The Perfect Collection is the only digital release of the original version of the series that is available in North America and Europe. While I would have preferred the higher quality releases of the original version, such as the Second Impact Box or the Archives of Evangelion DVD Box, those releases simply aren’t practical because of their lack of accessibility, both to myself as well as to the masses (although I’d like to do subtitles for the Archives of Evangelion at some point, if I can find the time).
I highly value authenticity and quality, but I simply could not deny that in this case, accessibility was a huge factor in making these subtitles a practical thing for people to try. I’m more than aware of the Perfect Collection’s reputation for substandard video quality (although I think much of this should be attributed to the first four episodes in particular), and I imagine the number of people interested in a project that uses it is probably diminished because of that reputation—but I bet the number of people who are actually able to try my project out would be even fewer had I chosen the Second Impact Box or the Archives of Evangelion DVD Box.
So of the commonly available releases, it was a choice between the Perfect Collection and the Platinum Edition, which ultimately meant it was a choice between story and video quality. The choice was an easy one for me to make: story always comes first. But I also prefer the original color palette before it was tinted blue, so that’s a small bonus.
It should be noted that while the Blu-ray Box is essentially an HD release of the edited version of the series, it does include an option for the original audio.