Systems for recombinant Adeno-associated virus (rAAV) production mimic (only) the lytic phase of AAV infection. Wild-type AAV biology is, however, more complex, which is reflected in the densely coded viral genome and the multiple functionalities of its viral replicases (Rep). This complexity is inherited by the recombinant system and may be disadvantageous for production yield and homogeneity. Using rAAV2-mKate2 based on a three-plasmid system as a model, we analyzed how rAAV genomic titer and empty capsid load, which is a major impurity, were influenced by modifications to the rep gene. Experiments included (i) site-directed mutagenesis of predicted post-translational modification sites of Rep, (ii) modifications at the genetic level to the largely unstructured Rep C-termini, as well as (iii) modifications to the rep regulatory elements. Site-directed mutagenesis did not influence the genomic titer but influenced the empty capsid fraction in both directions, with mutant Rep52/78 S535A and a variant with only Rep40/68 (R532G) increasing the proportion of full capsids. At the rep regulatory level, variants close to the wild type had the highest genomic titer, including those with a wild-type Kozak sequence and a p5 TATA-box, a composition not always implemented in common producer plasmids. The results also revealed that presumed unrelated sequences in the plasmid backbone influenced the genomic titer. Together, the findings validate the rep gene cluster and its proteins as targets to simplify and improve rAAV production, e.g. by reducing the number of required replicases or by increasing the fraction of full capsids.