This is not a complete answer, but is to long for a comment.
There are several issues with such a definition of basis. In general, we can expect an uncountable basis to be indexed by some set $\Omega$ and if we want a definition of basis as you wish, we need to integrate over $\Omega$, that is $\Omega$ can be, for example, a measure space, and the integral used to define the expresion of a vector as a ''linear combination'' of vectors in this basis is a Bochner integral.
But let me be more concrete. Imagine we have a basis $\{v(t)\}_{t\in I}$, where $I$ is some interval, of a Hilbert space $H$ and we have the property that for all $v\in H$ there exists a function $a:I\to\mathbb{F}(=\mathbb{R},\mathbb{C})$ such that
$$
v = \int_I a(t)v(t) \; dt.
$$
In the case of Hilbert spaces we are specially interested in the case of orthonormal bases, so let's assume we have some sort of Gram-Schmidt procedure in this case so we can effectively obtain an orthonormal basis (or perhaps we need to invoke Zorn's lemma). So assume that $\langle v(t),v(s)\rangle = \delta_{ts}$, there $\delta_{ts}$ is the Kronecker symbol. Then we have, for $r\in I$, an expression of the form
$$
v(r) = \int_I a(r,t)v(t)\; dt
$$
and consequently
$$
1 = \|v(r)\|^2 = \left\langle \int_I a(r,t)v(t)\; dt,\int_I a(r,s)v(s)\; ds \right\rangle = \int_{I}\int_I a(s,t)a(r,s)\langle v(t),v(s)\rangle \; dt ds,
$$
where I used the expeted bilinearity property of the inner product. Now let $\Delta=\{(t,s)\in I\times I \; | \; t=s\}$ and let
$$
\chi_\Delta(t,s) = \begin{cases}
1 & \text{if } (t,s)\in\Delta,\\
0 & \text{if } (t,s)\not\in \Delta.
\end{cases}
$$
Then we obtain
$$
1 = \int_I\int_I a(r,t)a(r,s)\chi_\Delta(t,s)\; dtds,
$$
but $\Delta$ is a set of measure zero, so this integral equals zero, that is $1=0$, which is absurd.
Thus at least we cannot hope to have such a theory of bases for Hilbert spaces with the property of having orthonormal basis.
Now, I cannot see the Fourier transform as an analog of a basis. To being with, the function $x\mapsto e^{itx}$ is not an element of $L^2(\mathbb{R})$ so we cannot expect this functions to be a basis of $L^2(\mathbb{R})$. So we need to restrict to functions in some bounded closed interval, $[-\pi,\pi]$ say. In this case we do have $x\mapsto e^{itx}$ as elements of $L^2([-\pi,\pi])$, but they are not orthogonal because under the inner product
$$
\langle f,g\rangle = \int_{-\pi}^{\pi} f(x)\overline{g(x)}\; dx
$$
they are not orthogonal: actually if $s\neq t$ we have
$$
\langle e^{itx},e^{isx}\rangle = \frac{2\sin((t-s)\pi)}{t-s}
$$
(I hope I made no mistake) which is different from zero unless $t-s$ is an integer. Thus we again arrived the issue that we loss an orthonormal basis.
I think this is maybe the tip of the iceberg (and maybe I'm wrong). I don't know if there are another patologies with such a notion of basis, and I know no reference about it.
To finish my (long) comment: We do have uncountable ortonormal basis for Hilbert spaces, but the definition is different: Any such basi $(v_i)_{i\in I}$ has the property that for all $v\in H$ there exists a countable subset $I'\subseteq I$ such that
$$
v = \sum_{i\in I'} \langle v,v_i\rangle v_i.
$$
(This is actually not the definition but a consequence of it.)