This answer is assuming you are not removing the private key $a$ from the computation of $S$, and instead actually meant what is said in the title of the question:
$S = r + a H(A, M)$
Removing $a$ from the computation would be terrible.
The first issue that comes to mind is malleability, on top of collision resistance.
The signature process for EdDSA actually goes as follows:
Input: message $M$, secret key bits $(h_0, h_1, \ldots, h_{2b-1})$,
basepoint $B$ and public key point $A$
- $a \gets 2^{b-2} + \sum_{3 \leq i \leq b-3} 2^i h_i$
- $h \gets H(h_b,\ldots,h_{2b-1},M)$
- $r \gets h\mod \ell$
- $R \gets r\cdot B$
- $h \gets H(R, A, M)$
- $S \gets (r + a h) \mod \ell$
Return: $(R,S)$
As you can see, if you do not include the value $R$ in the hash $h$, the value $S \gets (r + a h) \mod \ell$ can easily be modified in a way that would allow to produce new signatures for the same message:
- pick a random $k$
- compute the point $R' = R + k\cdot B$
- compute the value $S' = S + k \bmod \ell$
And you now have a new, different signature $(R', S')$ for the same public key $A$ that will verify for the message $M$.
This is possible because the value $r$ behind computed with the secret key, it is not meant to be public and is not necessary for verification. This property was used in a fault attack in 2017.
Malleability is not necessarily unwanted in cryptographic scheme, but is often frowned upon since it can very easily lead to issue with implementations.
Threshold cryptography is rough and full of dangers, and I wouldn't advise coming up with a malleable scheme as these have already proven to cause issue with threshold schemes.