Especially considering how much the writers made Shepard shoulder throughout the trilogy. There's just no way to outdo saving the entire galaxy and deciding the fates of multiple species, and it's not something that should ever be attempted, in my opinion. It just becomes total epic-bloat.
Yeah, Shepard should have never been given the ability to cause the extinction of the Rachni, Krogans, or the Quarians/Geth. Even 'little' things like determining whether the Hanar home world gets left completely vulnerable to Reaper attack is pushing it too far (IMO). Allowing the protagonist to have the option to completely remove a species from the setting not only leads to epic bloat (like you said) but also makes carrying forward a consistent world state and narrative an absolute nightmare.
Either you have to completely ignore the species that could have died or you have to make up replacements to fill in that gap, and seeing the treatment of our ME 2 squad mates in ME 3; especially the 'Not-Mordin' and the 'Not-Legion' characters; I would much rather have BioWare retcon the canon and say that "This race is alive." or "This race is dead." then have to deal with the 'Not Krogans' or the 'Not Quarians'.
Personally, I would go with a world state where we have as many species alive as possible; even the Rachni; simply because it adds much more diversity to the setting with all of these different alien species; and in the Rachni's case, it helps keep an 'alien' alien present rather than everyone being rubber fore-headed humans, because lets be honest, BioWare's track record at adding truly alien species to the setting has diminished over the course of the trilogy.