I’m sure that if you only talk about storing binaries from “mvn deploy” both will do fine.
We use Artifactory very extensively with all upgrades along the way. Lots of projects, numerous snapshots deployed and external repos proxied. Not a single problem. I find it hard to explain how other people experience issues with its DB, indexing or anything else. Nothing like that ever happened to us. Also, Artifactory allows to store data on a disk and only use a DB for storing metadata, it is quite flexible (see more here).
What makes those applications very different is their approach towards integration with other build tools and technologies. Nexus and Sonatype are pretty much locked on Maven and m2eclipse. They ignore anything else and only recently started to work on their own proprietary Hudson integration (see their Maven 3 webinar).
EDIT: This is not true anymore as of 2017 Nexus gives a much larger support for other build tools End of Edit
Artifactory provides an awesome Hudson, TeamCity and Bamboo integration, and Gradle / Ivy support. So while Nexus gives you nothing once you step out of Sonatype “comfort zone” (Maven, m2eclipse), Artifactory embraces and collaborates with all major build tools.
In fact, being able to deploy build artifacts from Hudson, when job has finished, and not by “mvn deploy” is a huge difference: Artifactory Hudson plugin makes an atomic-like deploy of all artifacts at once, only when a build job finished successfully. “mvn deploy” runs after each module and can deploy a partial set of artifacts if a build job fails in the middle. Deploying from Maven on module completion and not from a build server on job completion is really a bad thing to do.
As you see, Artifactory thinks “outside the box” while Nexus thinks “inside the box” and only cares about Maven and Maven artifacts.
Something else that makes Artifactory more accessible is their cloud-based Artifactory Online solution. For about $80 a month you have your own Artifactory instance, no need to dedicate any server for it.
Artifactory has a simple and straightforward REST API, don’t know how it works for Nexus.
Edit Nexus has also a REST API that you can use easily as well.
To summarize, for basic storage of Maven artifacts I think both are fine. But while Nexus stops there being strictly a “Maven repository manager”, Artifactory goes on and on, being a general “Binaries storage” for binaries of any kind, from any build tool and CI server.