I used Netlogo a lot and I found it is not constraining anything I want to build. However, I am interested to learn Java based ABS for bigger engineering project. One of the key question is if there is a agent type as link (directed and undirected) and supports the related primitive commands (methods) for easy usage? (see https://ccl.northwestern.edu/netlogo/docs/dictionary.html#linkgroup)
There are a few ways to use networks in Repast Simphony. One is through the network projections, where the network, rather than an individual link, is an object with methods used to add and remove links between agents (see the Repast Java Getting Started Guide).
Another method is through the ReLogo language, where links are agents with primitives (see the ReLogo Getting Started Guide). Based on your interests in "bigger engineering projects" I'd recommend the first, Java-based approach, as that will be much more performant and scalable.