The crossover should definitely go both ways... Because once you know that there are hundreds, maybe thousands of people with superpowers running around unaccounted for, that raises the stakes for Civil War tremendously, in an organic way. Civil War can be about Thaddeus Thunderbolt Ross worrying exclusively about a tiny handful of people, who are mostly ex-soldiers and ex-operatives, or it can be about Ross and his people having a concern about superpowered people in general. And in that scenario, the Avengers are just the most visible and highly skilled tip of the iceberg. Which one sounds more interesting to you?