The Borel sigma algebra on $\mathbb{R}$ is obtained by starting with open sets in $\mathbb{R}$ and repeatedly applying the operations of complement, countable union, and countable intersections. My question is, what would happen if you don't just allow countable unions and intersections, but also allow unions and intersections of $\aleph_1$ many sets?
Now obviously if we assume the Continuum Hypothesis, the answer is "we obtain all subsets of $\mathbb{R}$". But we just assume $ZFC$, then what sets do we know we can obtain? Can we at least obtain all Lebesgue measurable sets? Can we still obtain all subsets of $\mathbb{R}$?
The system of sets you've described is the $\omega_1$-Borel hierarchy. I don't know who first introduced it, but Arnie Miller has a bunch of work on it and related topics - see e.g. this article and this set of notes.
This is well outside my comfort zone, so let me just say a brief bit about one of the very basic questions (cribbing horribly from page $2$ of Miller's aforementioned paper, and using his notation): can we get all the sets, and if so when? Of course, we need to assume $\neg$CH for anything interesting to happen.
Steprans showed that it is consistent that $\Pi_3^*=\Sigma_3^*=\mathcal{P}(2^\omega)$, but $\Pi_2^*$ and $\Sigma_2^*$ are incomparable proper subsets of $\mathcal{P}(2^\omega)$. I don't know anything about his proof, but Miller mentions that the model it produces has $2^\omega=\aleph_{\omega_1}$, and Carlson showed that in order to have every set be $\omega_1$-Borel we must have $cf(2^\omega)=\omega_1$. So in some sense, "Every set is $\omega_1$-Borel" does have a "CHy-flavor."
Steprans further observed that ZFC+$\neg$CH implies that we can't have $\Sigma^*_2=\mathcal{P}(2^\omega)$. For suppose $A$ were a $\Sigma^*_2$ set of size $>\omega_1$ (which must exist since CH fails). Then as a union of $\omega_1$-many closed sets, it must contain an uncountable closed set and hence a perfect subset. But now consider any Bernstein set of cardinality continuum.
Finally - and this is Miller's own result - Martin's axiom at $\omega_1$ alone implies that the hierarchy doesn't collapse; however, ZFC+$\neg$CH alone doesn't obviously tell us even that $\Pi^*_2\not=\Sigma^*_2$ (Miller lists this as open).
As mentioned above, this is far outside my range of literacy; please let me know if I've made any mistakes!