As indicated in the comments, the greatest class of rank 2 3-manifolds (including rational homology spheres) are the genus 2 manifolds, which as indicated by Ruberman are double branched covers over links (coming from the hyperelliptic involution of the genus 2 surface which extends over both handlebodies). This includes connect sums of lens spaces and all the spherical space forms, as you indicated. However, it was a celebrated result of Boileau and Zieschang that there are certain Seifert-fibered spaces with rank 2 fundamental group, but Heegaard genus $=3$. They completely classified the rank 2 Seifert fibered spaces. These examples were extended by Weidmann and Schultens-Weidmann to certain graph manifolds (with rank $2$ fundamental group and genus $>2$). I think the state of the art in the non-hyperbolic case is a partial classification theorem of Boileau-Weidmann.
It is still unknown whether 2-generated hyperbolic 3-manifolds have Heegaard genus 2. Thurston observed that such manifolds are also branched covers over a link in $S^3$. Also, certain finiteness results are known for hyperbolic manifolds with rank 2 fundamental group, genus $>2$, and injectivity radius bounded below which has been written by Souto.