This may not be as straightforward as it looks.
In one way, just making synonyms is ok. This, as you mentioned, will help to group up questions instead of splitting them to 100 different tags. For example, Code Geass R2 can effectively be a synonym of Code Geass (I see no problems with this; if anyone does, please tell me).
On the other hand, this definitely can not be used blindly for each and every series.
For example, we have FMA and FMA:Brotherhood. Making them synonyms would be (in my opinion) a huge mistake, since the series' stories are just different, and it's even possible that the same question can be answered differently depending on whether it is related to FMA or FMA:Brotherhood.
So I would say that if the suggested synonym can not possible confuse the question-posters and the answerers, it's acceptable. But should rather be handled manually for each specific tag, because there's really no rule of thumb here.