For deep space missions there's rarely any stage at all. It's usually a probe launched into cislunar space using standard cislunar stages, and then the probe uses its own propulsion system to reach its destination in deep space, no separate stage for that. But then, there could be a standarized system/platform for deep space propulsion, which isn't a stage, just a standarized probe module.
While we got around to get a pretty consistent set of launchers, the development work for deep space propulsion is constantly ongoing. There are dozens of various ion engine designs, more or less standarized RCS propulsion systems, alternative propulsions like solar sail, and so on. It's all very much a work in progress - practically each new mission on top of the new mission goals is testing a new propulsion system.
So while creating a common, standard deep space propulsion system would come with some benefits, it would come with one critical disadvantage: depriving us of test platforms for new deep space propulsion systems. Any probe flying on the new standarized platform would be NOT testing a new, newly developed propulsion system.
Maybe once the development reaches some stalemate/cooldown situation where not much new can be designed and new designs will cease to sprout more frequently than new deep space missions occur that will make sense. If, similarly to current chemical engines, we reach a situation where there's quite hard to invent anything significantly better than existing designs, where developing a new platform around the new engine is less beneficial than going with "tried and true" (because the incremental advantages of the new engine aren't a significant improvement over the old), such platform - a standarized propulsion system for deep space - will become considerably advantageous. Currently there are simply too many good, new, untested systems and systems even better (and considerably so!) still in development to justify freezing the progress through adopting one standarized platform.