The biggest issue with this idea is the speed of light. Atoms participate in a lot of interactions because subatomic particles act nearly instantaneously. There are millions of interactions occurring within a single proton at any given moment, with various virtual particles annihilating one another. Even if you increased the time scale, space is extremely large and there just wouldn’t be a lot happening in a solar system. There would be slight perturbations in orbits, and the sun would go through cycles quickly, but it’s extremely stable when compared to an atom.
Then if you look on a galaxy-wide perspective, the actions within the solar system are irrelevant to most of the galaxy. It would take a hundred thousand years for even the sun burning out to register, and more than likely it wouldn’t even matter for any other solar systems in our area.
Then if you look beyond galaxies, it’s mostly just the intergalactic medium being siphoned one way or the other, with only the random movement of galaxies determining anything.
Atoms have the weak and strong nuclear forces, as well as electromagnetism to create the complexity of the universe. Solar systems have little else but gravity, constrained by incredible distances even on the scale of the speed of light.
Subatomic particles are still constrained by the same speed of light as larger objects. As you scale up the speed by which this recursive universe operates in, this limit becomes more and more significant, and fewer interactions can occur in the relative unit of time.
To put it another way, if this super-universe were to use solar systems as atoms, the speed of light would mean their timescale would be in the billions of our years to their seconds. This is derived from the picosecond delay of forces acting between our atoms and scaling up to the solar system “atoms” that make up our galactic neighborhood (10-100 light years apart). So solar systems couldn’t be atoms on this timescale because they would do little but coalesce some of the intergalactic medium and die in seconds.