Yes, keep it (but possibly change to [edition-comparison])
This tag adds value to the site and should stay.
Personally, I enjoy seeing questions about edition comparison and sometimes browse the tag just on its own to get a sense of how games change between editions (I wonder if those in the industry who are considering making a revised version of a game they have already published might find this valuable too).
Aside from that, here's why I think it should stay.
This isn't a meta-tag
The most common argument for removal is that it's a meta-tag, which have been discouraged before this site's creation.
The reason meta-tags are a problem is that they do not describe the content of the question. They describe some other aspect of the question, like the author's skill level, or the author's motivation for asking it, or generally what "kind" of question it is (poll, how-to, etc.).
Unlike tags such as [beginner], this tag does describe the content of the question, which is that it's wanting to know about different versions of the game.
The most commonly cited point from this article is the criteria that "If the tag can't work as the only tag on a question, it's probably a meta-tag." First off, I'd like to point out that it says probably, not automatically. In this case, I believe that a version question does accurately describe the content of the question. It tells us that it is about an aspect of the game (in this case, the comparison between editions) and helps clarify the scope. I think that removing it would be a detriment to the clarity of the question.
For what it's worth, we have a number of tags on this site that also are not able to be standalone, but provide a great deal of value to this site, such as openings, house-rules, variants, kids, and teaching. Other large sites have similar tags, such as Sci-fi/Fantasy SE where [lightsaber] is not a meta tag despite the fact that any questions about it by necessity require [star-wars]. Contrast this with tags like [beginner], [subjective], or [best-strategy], which don't provide a similar description of the question content.
Other established Stack Exchange sites have virtually identical tags
That said, I recommend renaming it to [edition-comparison]
One criteria for a meta-tag in the aforementioned link is that "If the tag commonly means different things to different people, it's probably a meta-tag". I do think that "version" is a bit too vague, especially compared to the two sites above. I think that migrating the tag to edition-comparison as RPG.SE does, would solve this ambiguity.