We shall not cease from exploration
And the end of all our exploring
Will be to arrive where we started
And know the place for the first time.
Through the unknown, unremembered gate
When the last of earth left to discover
Is that which was the beginning;
At the source of the longest river
The voice of the hidden waterfall
And the children in the apple-tree
Not known, because not looked for
But heard, half-heard, in the stillness
Between two waves of the sea.
Quick now, here, now, always—
A condition of complete simplicity
(Costing not less than everything)
And all shall be well and
All manner of things shall be well
When the tongues of flame are in-folded
Into the crowned knot of fire
And the fire and the rose are one.
--Little Gidding, T.S. Elliot

Comments
You could try constraining it by rating, perhaps? Selecting General Audiences or Teen as your rating would probably knock off a lot of the pairing fic. You'd still have to search through what's left, but it would eliminate the non-worksafe, at least. :D
(I've actually selected both gen and something else when I'm tagging stuff at times, usually because a story's basic plotline is gen but it also contains a pairing or a shippy chapter or two. The thought hadn't occurred to me that it might make it hard to search for things, though!)
I can understand tagging both when it's a mostly-gen story with a non-explicit shippy chapter or two. But today, it's like-- I was getting into the tags and they were things like "knifeplay" and "pegging" and, oh, "Alex/Hank Bathroom Stall Sex"-- and I start going wtf?? I know gen can be hard to define, sometimes, but surely that's not it?!
And yeah, the AO3's search features are still very beta-feeling. The inability to filter out search results and the fact that you can still only return 1000 results for a given search are the big problems I'm aware of.
Fusions-- hmm, I don't know what I think about that! I can both see myself getting irritated at there being fic in there with the wrong characters, but on the other hand, if they were both fandoms I was interested in, I might click. It's another case where being able to exclude tags in your search would help, I guess, so you could specify only your fandom and no others, or no AUs, or whatnot.