Aptly is a piece of cake compared to reprepro, because of the REST API. I just run it on a separate box, and make curl invocations from Jenkins jobs to post debs to it at the end of the build.

Depending what it is you're building, using the proper debian tooling (dpkg-buildpackage, etc) is not that much harder than FPM, and cooperating with the system gives you a lot of goodies for free (sourcedebs, cowbuilder, etc).