There should be lots of these, even with the second condition. So many that I can't imagine a classification. I'll call a $4$-cycle a square.
One construction is as follows: Start with an appropriate connected graph such that
- Each edge is on a unique square
- All vertices have degree $2$ or $4$.
- Two $4$-cycles have at most one vertex in common.
Then identify various degree $2$ vertices in pairs without making any new squares. So appropriate means you can do this. For example take an $N$ cycle for $N$ not too small, and attach a square to each edge. You could even take several of these and glue them together at vertices (in a sort of tree structure.) Here is a $12$-cycle decorated with squares and an extra square glued on just to show that we could grow this out in a wild variety of ways. I think in my identification of degree two vertices I did not create any new squares.
The examples below are included because they look nice and are already in the comments. The graph at the top right meets my three conditions if the two red edges are deleted. I am confident that the degree $2$ vertices could be identified in pairs without creating any new $4$-cycles.
With the red edges one has four vertices of degree $3$ along with two edges not in a square. One could take a mirror image of that graph and add $4$ more edges to connect them, create two more squares and bring the degrees up (there are also easier remedies such as using two more edges to make a square with the red ones.)
I previously had a claim about the graph with the octagons which was too optimistic.It has $42$ edges missing and I won't specify how to draw them. In each half (ignoring the two curved edges) there are $22$ deficient edges which do not belong to a square and connect vertices of degree $3.$ I thought that one could connect corresponding degree $3$ vertices in each half. I now see that that would put the edge $AD$ on the left into two squares. I've indicated a different match for edge $CD$ and imagine that it is not hard, with a little care, to match up deficient edges on the left with those on the right to create just enough squares. I don't think one needs to preserve orientation. The bottom (fragment of a) graph could probably be treated similarly. One could even try to match up deficient edges without adding any new vertices.