I don't know if this is exactly what you're looking for (and there's a good chance you already know what I'm going to write) but let me give it a try:
The realization functor of cyclic sets (not spaces!) to S1-spaces can be made part of a Quillen equivalence for two of the three commonly desired model structures on S1-spaces: The model structure that gives you "Spaces over BS1" is given in a 1985 paper of Dwyer-Hopkins-Kan, while a model structure that gives you the equivalences that you want (i.e., checked on fixed sets for finite subgroups) is given in a 1995 paper "Strong homotopy theory of cyclic sets" by Jan Spalinksi.
(Irrelevant to your question, but along the same lines: A recent paper of Andrew Blumberg describes how one can throw in some extra--still combinatorial--data and obtain a combinatorial model of the third desirable model structure on S1-spaces, namely where equivalences are those that induce equivalences on fixed sets for all closed subgroups.)
Spalinksi's model structure depends on the following construction of |X.|Cn (as a space-over-BS1) in terms of the subdivision construction: The simplicial set (sdrX)n=Xr(n+1)−1 has an action of Cr--since Cr is a subgroup of the copy of Cr(n+1) acting on Xr(n+1)−1; taking fixed points (in sSet) and then realizing gives |X.|Cn.
This suggests (though I haven't checked too carefully) that remembering each Xn as a Cn+1-space (in the sense you suggest, with subgroups) is enough, as you expected.
Now begins the speculative (and probably wrong) part of this answer: I have nothing too certain to say about writing this as a functor category, but it doesn't seem too unreasonable (to me, right now, at least) based on the above simplicial subdivision construction that we might be able to construct a reasonable candidate: some sort of mix of the cyclic category and the orbit categories for the cyclic groups. Purely combinatorially, this seems to get tricky.
But, I think we can realize this geometrically: Let (S1)r be the circle equipped with a mathbbZ action given by the rotation by 2pi/r. We could try to define Hom′([m−1]r,[m′−1]r′) along the lines of "(htpy classes of) degree r′/r, increasing mathbbZ-equivariant maps S1toS1 sending the mr-torsion points to the m′r′-torsion points". This should correspond to taking all the r-cyclic categories and sticking them together, and in particular is bigger than what we want. But, the mathbbZ-action on the circles should induce one on the Hom′-sets and the composition should respect it. Taking the quotient, we seem to get something that looks like a reasonable candidate. For each fixed r, we should be getting a copy of the cyclic category. And, e.g. Hom([m−1]r,[mr−1]1) should contain Homorbit(Z/mr,Z/r). (Disclaimer: It's late and I haven't checked any of this too carefully!)
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