From a gameplay perspective, the system added depth to missions where more than one appeared. I wish there were more that used all three characters at once, because those are by far the best missions.
From a story perspective, it's strange that people are saying they felt there weren't enough missions to get to know the V characters, then immediately say that they connected with Luis and Johnny. After all, they have as many missions, in fact more once you add the Strangers and Freaks missions. Not only that, you have their LifeInvader accounts, which tell you a lot about the V character's backgrounds.
Simple. Those 2 characters have their own story (other than IV's story from a different perspective). That's why in V some people can only connect with Michael, since he was the one with the most *storyline* mission he appeared on.
The whole story of V pretty much focused on FIB/IAA rivalry and MTF relationship. And how did the trio got involved in FIB/IAA? Michael's connection.