Our mental pictures of diffeomorphisms are already vague - it's not like our mind has graphing softwhere in it that plots specific points with a high level of precision, it just has a general idea of some stretching and bending and so forth - which means we already implicitly interpret two diffeomorphisms as essentially the same if they are sufficiently close.
One way to formalize this a bit is to pick a sufficiently small neighborhood $U$ of the identity, then declare $a\sim b$ (meaning "$a$ and $b$ are essentially the same") whenever $a,b\in U$, then translate this relation by declaring $a\sim b$ whenever $a,b$ are in some translate of $U$. If we want to extend this to an equivalence relation, that forces us to declare $a$ and $b$ to be related if one can be obtained from the other by a sequence of more or less negligible perturbations, even if the sum total of the perturbations may not be something we'd intuitively accept as negligible. That may be paradoxical, but this paradox is hardly unique to this situation: it's called the sorites paradox.
I think we do lose interesting information in the process. Certainly the mapping class group is coarser than the diffeomorphism group. For instance, rotating a 2-sphere around an axis by a really small angle is essentially the same as the identity, but doing it a large number of times exhibits a nontrivial loop in the diffeomorphism group which the mapping class can't see. In other words $\pi_0$ doesn't know anything about $\pi_1$. Just because it's a lesser amount of information doesn't change it's being an interesting feature, though.
If we forget the fact we're talking about diffeomorphism groups for the moment, hypothetically someone could apply the same sort of skepticism to any topological invariant which blurs together things that are sufficiently close and then accepts the formal consequences of the blurring. One could ask, "why should I consider two points that are close together in a space approximately the same, why is that an interesting thing to do?" as a reaction to the idea of taking the $\pi_0$ of a space, but ultimately knowing how many connected components a space has seems like a pretty fundamental feature of the space doesn't it?
Going back to the situation of topological groups of transformations on a space, consider how we think about smaller groups of transformations, namely Lie groups. Like, $\mathrm{O}(n)$ has two components - one for rotations, one for reflections, which are fundamentally different transformations. Indeed, an indefinite orthogonal group $\mathrm{O}(p,q)$ has four components, and it means something that $\pi_0$ looks like Klein four instead of cyclic order four.