I feel that we need a change. Our current policy on this makes things a bit vague and just seems lazy overall. I feel that the mods share some of the blame in their lack of action on the matter.
Because this has been brought up multiple times, it's about time we make an attempt to take action on the matter. Just putting it off til later merely delay the inevitable.
Why should I care?
First off, I personally think it makes for bad policy to have the tags be inconsistent. It feels a bit lazy to lump the whole of one series with different continuities under just the umbrella of one tag. Having multiple tags to differentiate a series will make it easier for both asker and answers as these questions will better establish the context of which series on is referring to. This will better confine the scope of the question to only that series, making most question easier to answer as you don't have to cover all the continuities if the OP doesn't specify.
Remakes and reboots fall under the same umbrella. Series like Hunter x Hunter and Ghost in the Shell often times change up the plot, alter scenes, and/or even add additional characters. Being able to make a distinction between the original from the remake can make answering one much easier, especially when you haven't seen one of them. This allows fans who are "experts" fans on one series to be able to seek out and cover the one that they are most familiar with.
What does this mean?
This doesn't mean every tag needs to be separated or be differentiated with an -anime, -manga, or -live-action suffix. It means we need to make a distinction between them. For example, by splitting fullmetal-alchemist into "fullmetal-alchemist-2003" and "fma-brotherhood" we can better focus on easy particular continuity and not have to specify which one we're talking about each time. It's the same logic as not needing to include the title series title in the question title when posting a question to reduce redundancy.
If a user asks about an event in a series with two different continuities (with a different outcome) and doesn't make a distinction as to which they are referring to, covering both might be require additional effort, especially if you've only seen one of them. It's a bit cumbersome to ask a Gundam Build Fighters specific question and need to differentiate it from the original Gundam or the Gunpla Builders Beginning G OVA, when all you have is the gundam tag. A tag should refer specifically to a particular series rather than the franchise as a whole.
What we need is a clear set of guidelines to abide by. The an older series shouldn't be given precedence over a new one. If the titles are the same, we should add a date to both. If the difference between a manga and an anime is somewhat minor (no major divergences in the plot [e.g., the Angelic Layer anime vs manga and the Akame ga Kill anime vs manga, compared to the Shomin Sample anime vs manga]), there should be no need to separate the two (i.e., they'll fall under one tag).
Should there be exceptions?
There may be special circumstances to warrant separation. For an example, Dragonball, Dragonball Z, Dragonball GT, and Dragonball Super can be different enough to warrant separate tags while being all a part of one continuous series with shared characters, compared to Naruto and Naruto Shippuden, which should not. The Fate/Stay Night falls in a similar category, we should refer to the Deen TV anime as separate from the Deen UBW, which is separate from the ufotable remake of UBW and Heaven's Feel. Evangelion should be separated into the TV series, End of Evangelion movie, and the Rebuild movies. This way we can make a distinction and better focus on the topic specifically, rather than generalize them.
What should we do?
I propose that if we would like split series with different continuities establish an meta where we clarify everything from the guidelines of how to approach tagging to any exceptions to these guidelines, along with an explanation of why decide to do things this way. This would eliminate any confusion on the topic and set a precedence for future series as well.
Less isn't always practical, but consistency and clarity are. While it may require more work (for the mods and community; retagging question, synonymizing, making better tag excerpts and wikis, etc.) as a whole, I feel that starting to be more consistent with our current site policies can better shape our attitude and outlook on future policies as well.