Let $\Omega$ be a bounded domain and define $V=L^2(\Omega)$ and $H=H^{-1}(\Omega)$.
Endow $H$ with the inner product $$(f,g)_{H} = \langle f, (-\Delta)^{-1}g \rangle_{H^{-1}, H^1}$$ where $(-\Delta)^{-1}g = \tilde g$ is the solution of $-\Delta \tilde g = g$ on $\Omega$, $\tilde g= 0$ on $\Gamma$.
In Lions' Quelques methodes... on page 192, he uses this set up to deal with a PDE of the form $$u_t - \nabla \cdot (|u|\nabla u) = f.$$
Now, we have a Hilbert triple $V \subset H \subset V^*$. I remember that we identify $H$ with its dual, but not $V$ with its dual. But $V^*= (L^2)^* = L^2$. So how should I think of the dual of $V$? I ask because Lions then says the following:
...standard theory from before tells us there is a unique $u \in L^2(0,T;V)$ with $u_t \in L^2(0,T;V^*)$ such that $$(u'(t), v)_H + a(u(t),v) = L(t)(v)$$ where $a(u,v) = \frac{1}{2}\int_\Omega |u|uv$
(and $L(t)$ is given but it's not relevant here). My question is, why does Lions write $(u_t,v)_H$ and not $\langle u_t, v \rangle_{V^*,V}$? We only know that $u_t \in L^2(0,T;V^*)$, don't know that it's in $L^2(0,T;H)$.
But if we did identify $V^* = L^2$, then we get $L^2 \subset H^{-1} \subset L^2$ (but this would mean $L^2=H^{-1}$!!!), and the duality pairing becomes the $H^{-1}$ inner product as defined above so it kinda makes sense.
Finally, any references to other work where PDEs are tackled with the pivot space equal to $H^{-1}$ with the inverse Laplacian are hugely appreciated. Thanks.
Most of this is repeated from my comments following the answer to this question, but the basic problem is here:
Actually, it's the other way around; it's ok to identify $V = L^2$ with its dual, but if we also insist on identifying $H$ with its dual, we have exactly the problem you observe: this then forces us to identify $H$ with $V$.
Now, on one level this is fine, because all separable Hilbert spaces can be identified (they're all isometrically isomorphic to $\ell^2(\mathbb Z)$), but whether or not one should do this is a different matter. In fact, you've demonstrated exactly why one should refrain from doing this: the identifications aren't compatible with the natural inclusions.
So really, we should be 'pivoting' around $V$, i.e. identifying $V$ with it's dual so that we have the inclusions
$$ H^* \subset V \subset H $$
Then, this will solve the concern you raise when you say
i.e. we will have $u_t \in H$ (to state it briefly) as well. Then, as you say
and our worries are taken care of.
If you have further concerns, let me know, and I'll try and address them.