"Tiny" Graph Isomorphism
[This is more of a few extended comments than an answer.]

1) If $GI \notin \mathsf{P}$, then there is no fixed-polynomial bound on the time complexity of all $\Pi_{M}$, even for $M$ that only take time, say, $n^3$: If for all time-$n^3$ $M$, $\Pi_{M} \in \mathsf{DTIME}(n^k)$, then the following is a poly-time algorithm for GI. On input $(G, H)$, construct a Turing machine $M_{G}$ with a clock which ensures that $M_{G}$ never runs for more than $n^3$ steps on inputs of size $n$, and such that $M_{G}(1^{|V(G)|}) = G$, and then solve $\Pi_{M_G}(H)$ in time $O(n^k)$. 

2) Since for any $M$, $\Pi_{M}$ is no harder than GI, one might think that the best result along the lines of "$\Pi_M$ seems not to be in $\mathsf{P}$" one could hope for is a GI-completeness result. However, it seems unlikely to me that any one $\Pi_M$ would be GI-complete, for at least the following reasons: 


All the GI completeness results I know of are for rather large classes of graphs, rather than having a single graph of each size. Even if you drop the efficiency requirement entirely, I do not know of any list of graphs $G_1, G_2, \dotsc$ such that $|V(G_n)| = n$ (or even $poly(n)$) such that testing isomorphism to $G_n$ is GI-complete.
On a related note, most (all?) GI-completeness results are not merely many-one reductions, but have the following form: there is a function $f$ such that given an instance $(G,H)$ of GI, $(f(G), f(H))$ is instance of the other GI-complete problem. (These are just poly-time morphisms of equivalence relations, or what Fortnow and I called "kernel reductions.) We can easily show unconditionally that there is no such reduction from GI to any $\Pi_M$ (even if you modify the definition to allow $M$ to output multiple graphs). Hint: Get a contradiction by showing that any such $f$ must have its image completely contained in $\{G_{M,n}\}_{n \geq 0}$.


3) Even though one could construct $M$ based on a universal TM as suggested in the question, perhaps one can still construct an efficient tester, just not efficiently. That is, maybe for each $M$, $\Pi_{M}$ is in $\mathsf{P/poly}$?