More Pragmatic Answer after Dialogue with OP in Comments
Rearranging the wave equation in the question to
$$\frac{d \vert \Psi \rangle}{dt} = \frac{i}{\hbar} H \vert \Psi \rangle \tag{1}$$
should make it obvious that wavefunction takes the form
$$\vert \Psi \rangle = e^{\frac{i}{\hbar} H t}. \tag{2}$$
However, the wavefunction is not only a function of time, but also of position. We can${}^\ast$ think about the time evolution of the system as
$$\vert \Psi(t) \rangle = e^{\frac{i}{\hbar}Et} \vert \psi_{r} \rangle, \tag{3}$$
where $\vert \psi_{r} \rangle$ depends on the position within some coordinate system and is independent of time, and $E$ generally represents the energy in the system, which is a scalar value.
We can now consider the time derivative of Eqs. (2) and (3) in the $\vert \psi_r \rangle$ basis,
$$\frac{d \vert \Psi \rangle}{dt} = \frac{i}{\hbar} H \,e^{\frac{i}{\hbar}Et} \vert \psi_{r} \rangle=\frac{i}{\hbar} E \, e^{\frac{i}{\hbar}Et} \vert \psi_r \rangle, \tag{4}$$
and rearrange to get
$$-\left( i \, \hbar \, e^{\frac{-i}{\hbar}Et} \right) \, \frac{d \vert \Psi \rangle}{dt} = H \vert \psi_{r} \rangle= E \vert \psi_r \rangle.$$
The second equality here is the eigenvalue equation. It follows directly that if we need energy to be real and positive, which we do, $H$ must have positive real eigenvalues. The eigenvalue equation above also implies that $H$ is diagonalizable. As noted in the comments to your question, these two conditions are sufficient to require that $H$ is Hermitian.
${}^\ast$ After thinking about this some more, I should point out that Eq. (3) amounts to an assumption that at least one eigenvalue of $\vert \Psi \rangle$ can be expressed as a function of time (independent of position). Similarly, Eq. (4) amounts to an assumption that the positional basis $\vert \psi_r \rangle$ is independent of time.
Einstein showed that these assumptions are only low velocity approximations, i.e. that time is not independent of space. This is one way of seeing why the Shrödinger equation is inherently non-relativistic.
Original Less Pragmatic Answer/Geometric Intuition Regarding Hermitian Matrices
The intuition behind Hermitian matrices, is that they are the "real" matrices in $\mathbb{C}^{n \times n}$. The most basic property of any Hermitian matrix ($H$) is that it equals its conjugate transpose $H=H^\dagger$ (in direct analogy to $r \in \mathbb{R}$ where $r = r^\ast$). Equally fundamental, a Hermitian matrix has real eigenvalues and it's eigenvectors form a unitary basis that diagonalizes $H$.
Those are the key mechanical properties, but they probably don't do much for intuition. I'll try to give a sense of the geometric role that Hermitian matrices play in complex spaces in hopes that it may help you intuit the more direct and less transparent explanations that you've probably already seen.
Consider the familiar case of generating a 1-sphere in $\mathbb{C}^1$ by taking the exponent $e^{i \theta}$, with $\theta \in \mathbb{R}$, such that $i\theta$ is a purely imaginary value. In this case, our implicit real basis for the real parameter $\theta$ is $1$, and not very interesting. If we wanted to be pedantic we could call $[1]$ a $1 \times 1$ Hermitian matrix.
In the same manner, we can generate a 3-sphere in $\mathbb{C}^{2 \times 2}$ by $U = e^{\frac{i}{2} \vec{\phi} \, \cdot \, \vec{\sigma}}$, where $\vec \phi$ is a vector in $\mathbb{R}^3$, and $\vec \sigma$ are the three Hermitian Pauli matrices (which are much more interesting than $[1]$). This guarantees that $U$ is an arbitrary element of $SU(2)$, which is isomorphic to the 3-sphere. Setting $\vec \phi = \alpha (\hat \phi_1, \hat \phi_2, \hat \phi_3)$, Taylor expansion gives
$$U=e^{\frac{i}{2} \vec{\phi} \, \cdot \, \vec{\sigma}}=\begin{bmatrix} \cos \frac{\alpha}{2} + i \hat \phi_3 \sin \frac{\alpha}{2} & \sin \frac{\alpha}{2} (\hat \phi_2 + i \hat \phi_1) \\ \sin \frac{\alpha}{2} (-\hat \phi_2 + i \hat \phi_1) & \cos \frac{\alpha}{2}- i \hat \phi_3 \sin \frac{\alpha}{2} \end{bmatrix}.$$
The elements of the Pauli basis generate a representation of the (real) Lie algebra $\mathfrak{su_2}$, and are related to the three independent rotations ($R_n$), by $\sigma_n = 2i \frac{\partial R_n}{\partial\alpha} |_{\alpha=0}$. Although $\sigma_2$ makes use of imaginary numbers, the Pauli basis is real in all the ways that matter. For example $\sigma_n^2 = I$ and $(\vec \phi \cdot \vec \sigma)^2 = \vert \vec \phi \vert^2$. Just as in the case of $i \theta$, when we multiply the $\sigma_n$ by $i$, they become purely imaginary, i.e. $(i \sigma_n)^2 = -I$ and $(i \vec \phi \cdot \vec \sigma)$ is isomorphic to the pure quaternions (the imaginary part of the quaternions).
Recalling that $\sigma_n^2 = I$, if we forgo the $i$ in the exponentiation, we get something directly analogous to the 1-dimensional case of exponentiating with the split complex number, $k^2=1$, where $e^{k \beta} = \cosh{\beta} + k \sinh{\beta}$. In the three dimensional case we have, by Taylor expansion again:
$$ V = e^{\frac{1}{2} \vec \phi \, \cdot \, \vec \sigma} = \begin{bmatrix} \cosh \frac{\alpha}{2} + \hat \phi_3 \sinh \frac{\alpha}{2} & \sinh \frac{\alpha}{2} (\hat \phi_1 - i \hat \phi_2) \\ \sinh \frac{\alpha}{2} (\hat \phi_1 + i \hat \phi_2) & \cosh \frac{\alpha}{2} - \hat \phi_3 \sinh \frac{\alpha}{2} \end{bmatrix}, $$
which are Hermitian matrices with unit determinant and Minkowski signature $(+,-,-,-)$. This matrix can be directly identified with a real 4-vector as discussed below. The 1-dimensional projection operators $\frac{1}{2}(1 \pm k)$ are also strikingly similar to the 3-dimensional Hermitian projection operators $\frac{1}{2}(I \pm \hat \phi \cdot \vec \sigma)$.
Pauli used his namesake matrices to formulate the Pauli equation, which is unfortunately non-relativistic since it fails to treat space and time on an equal footing. One of Dirac's great breakthroughs was generalizing the Pauli matrices into the gamma matrices, which enabled him to formulate the Dirac equation, which was one of the great breakthroughs of the past century.
Attempting to explain Dirac spinors at an intuitive level would be quite a task (I can provide some good references if you like), but we're only a breath away from coordinate generating spin matrices, which provide great insight into the value and necessity of Hermitian matrices. This is largely due to Wheeler's great presentation of them in Section 41.3 of Gravitation, which I highly recommend.
Essentially if we take a direct sum $\mathfrak{su}_2$ (which generates the element $U$ above) with $i \mathfrak{su}_2$ (which generates $V$ above) we get the 6-dimensional (complex) Lie algebra $sl_{2 \mathbb{C}}$, which generates the universal cover of the Lorentz group $SL(2,\mathbb{C})$, providing both Lorentzian rotations ($U$), boosts ($V$) and combinations of the two ($L \in SL(2,\mathbb{C}$)). In other words, any $L$ has unique left and right polar decompositions as $UV_R$ or $V_L U$, where $V$ is analogous to a radius, and $U$ to an angle. ($U$ and $V$ commute iff they share the same unit vector $\hat \phi$).
Wheeler calls the matrix $L$, which effects an arbitrary Lorentz transformation, a Lorentzian spin transformation matrix. $L$ acts on an Hermitian "coordinate-generating spin matrix" ($X$),
$$X=\begin{bmatrix} t + z & x-iy \\ x+iy & t-z \end{bmatrix},$$
(note the same Hermitian structure and Minkowski signature as $V$) according to $X^\prime = L X L^\dagger$.
The structure $X$ and $L$ ensures that $X^\prime$ remains Hermitian by
$$ (X^\prime)^\dagger = (LXL^\dagger)^\dagger = (L^\dagger)^\dagger(X)^\dagger(L)^\dagger = LXL^\dagger = X^\prime $$
and thus $(t,x,y,z) \mapsto (t',x',y',z')$ remains real.
I'm not sure I answered the question, as I didn't say much specifically about Hamiltonians, but in some sense that boils down to Hamiltonians describe real things (specifically kinetic energy + potential energy of a system) in complex spaces, and Hermitian matrices are mathematical representations of real things in complex spaces. Alternative explanations sometimes take forms like (quoting Weyl) "In an infinitesimal unitary rotation of a vector field the velocity $\frac{d \chi}{d \tau}$ is related to $\chi$ by by means of a correspondence whose matrix is i times an Hermitian matrix."
Hopefully the color above about the role Hermitian matrices play in complex spaces helps make sense of the generally unintuitive direct answers to your question.
EDIT: I forgot to answer the bonus question. The Pauli matrices are both unitary and Hermitian. The Hadamard matrix,
$$\begin{bmatrix}\frac{1}{\sqrt{2}}&\frac{1}{\sqrt{2}} \\ \frac{1}{\sqrt{2}} & -\frac{1}{\sqrt{2}} \end{bmatrix}, $$
which is prominent in QIS/QIT, is also unitary and Hermitian.