Let $F$ be a real quadratic field and let $E/F$ be an elliptic curve with conductor 1 (i.e. with good reduction everywhere; these things can and do exist) (perhaps also I should assume E has no CM, even over F-bar, just to avoid some counterexamples to things I'll say later on). Let me assume that $E$ is modular. Then there will be some level 1 Hilbert modular form over $F$ corresponding to $E$. But my understanding is that the cohomology of $E$ will not show up in any of the "usual suspect" Shimura varieties associated to this situation (the level 1 Hilbert modular surface, or any Shimura curve [the reason it can't show up here is that a quaternion algebra ramified at precisely one infinite place must also ramify at one finite place]).
If you want a more concrete assertion, I am saying that the Tate module of $E$, or any twist of this, shouldn't show up as a subquotient of the etale cohomology of the Shimura varieties attached to $GL(2)$ or any of its inner forms over $F$ (my knowledge of the cohomology of Hilbert modular surfaces is poor though; I hope I have this right).
But here's the question. I have it in my head that someone once told me that $E$ (or perhaps more precisely the motive attached to $E$) should not show up in the cohomology of any Shimura variety. This is kind of interesting, because here is a programme for meromorphically continuing the L-function of an arbitrary smooth projective variety over a number field to the complex plane:
1) Observe that automorphic forms for GL_n have very well-behaved L-functions; prove that they extend to the whole complex plane. [standard stuff].
2) Prove the same for automorphic forms on any connected reductive algebraic group over a number field [i.e. prove Langlands functoriality]
3) Prove that the L-functions attached to the cohomology of Shimura varieties can be interpreted in terms of automorphic forms [i.e. prove conjectures of Langlands, known in many cases]
4) Prove that the cohomology of any algebraic variety at all (over a number field) shows up in the cohomology of a Shimura variety. [huge generalisation of Taniyama-Shimura-Weil modularity conjecture]
My understanding is that this programme, nice though it looks, is expected to fail because (4) is expected not to be true. And I believe I was once assured by an expert that the kind of variety for which problems might occur is the elliptic curve over $F$ mentioned above. At the time I did not understand the reasons given to me for why this should be the case, so of course now I can't reproduce them.
Have I got this right or have I got my wires crossed?
EDIT (more precisely, "addition"): Milne's comment below seems to indicate that I did misremember, and that in fact I was probably only told what Milne mentions below. So in fact I probably need to modify the question: the question I'd like to ask now is "is (4) a reasonable statement?".