I'm semi-strong against option 2. I understand your point (even though I haven't watched Rebuild), but I think it's kind of annoying if we have multiple tags for series that are in the same franchise, even if one is a reboot of the other or significantly different from it. Whenever I write a question about Fate/Zero, I'm afraid people will miss it if I don't also tag it Fate/Stay Night, so I add both tags, which just feels like an unnecessary extra step. And I would definitely add the Fate/Stay Night tag if I were asking about one of the more obscure properties, like Strange Fake, or even Kaleid Liner Prisma Illya, because the chances are pretty good that people who know about Stay Night know about these others, and I would want to make sure those people saw my question. Maybe I'm just paranoid.
The other thing is, I assume that certain questions will apply to or solicit information about both the original and Rebuild. E.g. your example "Did Shinji and Kaworu ever kiss?"; the questioner might want to know if it ever happened in any of the original, Rebuild, the original manga, the Angelic Days manga, or the Girlfriend of Steel video games. Personally, if someone asked "Did Shinji and Kaworu ever kiss in Rebuild?" and I was going to write an answer, I might also mention whether it had ever happened in Neon Genesis, just for the sake of completeness. (For example, "No, they never did in Rebuild, but in Neon Genesis...")
So I only see the putative Rebuild tag being useful for narrowly focused plot questions, and I expect that most of those questions will have to mention some context, which usually begins "In Rebuild of Evangelion movie x.yy, ..." I just don't see it as being that confusing for Rebuild questions to be tagged neon-genesis-evangelion, even if it is a different story and different continuity. That goes double if we go with option 3 and make an evangelion tag.
SciFi and Fantasy SE takes the approach of having separate tags for related properties. For instance, they have a Star Trek tag, a Star Trek TOS tag, a Star Trek TNG tag, and so on for all the bajillion Star Trek properties. The Star Trek tag acts as sort of a "One Tag to Rule them All" in that every single question related to Star Trek appears to have this tag, and tags for The Original Series, The Next Generation, etc. are added as necessary. This is sort of a compromise between your option 2 (with completely separate tags for the original and Rebuild) and option 3 (with a single general tag). It wouldn't be my personal preference, for the reasons I stated above, but it would suit me better than straight option 2, where the two separate tags are officially unrelated and one of them (probably the NGE tag) most likely ends up becoming the One Tag.