There are four profound problems:
1. The first is philosophical.
GR is classical, with smooth continuous fields, locality and determinism*.
QM has superposition, entanglement, non-locality and indeterminism.
GR seems more intuitive, but QM seems more of an irreversible revolution, so slight win.
2. The second is philosophical.
GR provides equations for how spacetime is warped by matter and energy (background independent).
QM assumes a static background 'stage' of spacetime
(wavefunction is a function of spaces,
Schrodinger Equation is a wave equation wrt time,
so background dependent).
GR seems deeper, QM seems superficial.
GR wins this hands down, QM has to change or be extended
to make it background-independent (perhaps see String Theory).
3. The third is philosophical.
QM has a 'measurement problem'. Wave: the Schrodinger Equation is linear,
unitary, time reversible and (hence) information preserving.
Particle: measurement is discrete, discontinuous, non-linear and
information destroying.
So there is either a bizarre mismatch between the two parts of the theory,
or you strike down measurement, and propose the Many Worlds interpretation,
which punts all the measurement problems into other causally disjoint
'worlds', without a clear way to establish probabilities.
This is purely a problem with incomplete/incoherent
explanation by QM. The fact that physicists cannot agree on an interpretation is damning (is the wavefunction real? is Hilbert space real? what is measurement?)
4. The last is practical. QFT is just Fourier Analysis where it true, and a terrible hack everywhere else: double quantization, renormalization of infinities, energy cut-offs, virtual particles, incomplete Standard Model (neutrinos?), why 3 generations, what is the vacuum (dark energy).
My scorecard is 40:60 draw in QM's favor, GR total win, and two QM no-contest own-goal losses. So a clear GR win, in the sense that a new integrated theory of Quantum Gravity will have:
- a copy of GR, even if it is emergent from discrete substrate
- radically overhauled version of QM
(philosophical, explanatory and model details),
even as predictions don't change much,
and some important philosophical revolutions are preserved
My own personal pure guess is that the next level substrate is discrete. The two signposts are: holography, dimensional reduction and AdS/CFT-ishness; and the huge clue that quantum entanglement seems to create relativistic spacetime (but perhaps not proper time).