Sorry I re-read your question and I misunderstood your confusion. It seems that you feel the equations lead to a contradiction with the definition of capacitance. This is because it seems you think a higher capacitance means more energy stored on the capacitor. From our equations for capacitance of an infinite capacitor:
$C = Q / V = Q / Ed$
$E$ is constant for infinite plates with charge uniformly distributed. If $E$ and $Q$ are constant and $d$ increases then it would appear that capacitance decreases so the capacitor's "ability to store energy" diminishes.
We know that energy for a capacitor is $U = \frac{1}{2} (QV) = \frac{1}{2}Q(Ed)$
Which would imply that as $d$ increases, $U$ increases which means the capacitor is actually storing MORE energy! This isn't a contradiction because while the energy stored by the capacitor went up, its ability to store energy is a different concept. $U$ and $C$ don't necessarily go up or down with each other. Its ability to store energy depends on its ability to store charge which depends on its geometry and distance to the other plate; not it's current level of energy storage. It's the capacitors size/shape that determines how much charge can be stored on it (its capacitance).
Here are some examples of expressions for capacitance of different shapes:
Parallel plate capacitor (for short distance $d$, area $A$ of plate):
$C = \epsilon\frac{A}{d}$
Coaxial cable ($l$ is length of cable, $R_{1}$ and $R_{2}$ is inner and outer radius):
$\frac{2\pi\epsilon l}{ln\frac{R_{2}}{R_{1}}}$
Each of these quantifies how much charge a capacitor can store (and thus how much energy it can store) and you'll notice they depend exclusively on the geometry of the capacitor AND the distance between the capacitors - $d$ for the parallel plate and $R_{1}$ and $R_{2}$ for the coaxial cable.
I think it's important to remember that infinitely sized plates don't exist. Plates are considered infinite either because they are so close as to appear infinite to each other or so big that moving further or closer makes no difference to their relative size to one another. But in reality, the "so big" infinite plate doesn't exist. We can get two objects so close to each other so that their electric field is constant in the region between them because the plates appear infinite in the region between them but we can't make an infinitely large plate.
Now, in the case of plates being so close as to appear infinite, when we move them further apart, they no longer appear infinite and $E$ doesn't remain constant; it decreases faster than $d$ increases because $E$ is an inverse square law (it is related to distance according to $\frac{1}{d^2}$). Which means $U$ and $C$ both decrease in that particular case.
Sorry for the hastily written answer. Let me know if you're still confused