Compare functional enrichment between genelists
To compare gene list based on gene ontologies you can use GOSemSim (Note, I'm a contributor to the package). You can select the semantic similarity to compare them, that is how the redundancies and hierarchical relations are counted. The main result you can obtain is similarity matrix for each comparison between gene lists. 

However if you perform a GO term enrichment and then you compare the gene list of each GO term by looking at which GO do they belong it won't be much useful. I would suggest you to use BioCor (I'm the developer of it), which can use any pathway information (such as the ones of Reactome) to asses if they are related to the same pathways.