I don't think the system should be changed, the problem is in people's perceptions of a small Free Company. The developers expect a small Free Company to be 10 members minimum, not 3 which is why you need that many members to create one in the first place. This misconception is also why there is a housing problem because they expected more people in a guild. They expected people to make communities, not cliques. If you want to privately chat with two friends, there are link shells for that so if you've chosen to ignore FC requirements, Square Enix aren't at fault.