The problem is that your party actually does get to visit a town and go unnoticed, Nautilus. I think what makes the whole "fugitive" element not work is that its not until Chapter 7-9 that the identities of the l'Cie are given to the public in a transmission. Your party could easily hide their tattoos (especially Lightning since hers seems to be in a sensitive area) and there are even scenes later in the game where Snow goes a bit unnoticed til he starts showing off and makes his tattoo noticeable.

Even the scene with Hope giving the girl her Carbuncle doll back, the towns folk only knew they were l'Cie cause Snow purposely told them and started a ruckus to get the people to riot earlier in that chapter. I really feel the game should have tried to be more forward with the player about explaining that everyone in Cocoon knew their identities. The idea they couldn't hide that fact gets crushed in Chapter 8 when Sazh and Vanille waltz into Nautilus like they didn't have a care in the world.

Ultimately, I think the lack of towns and NPCs definetly hurt the title. It does create a sense of isolation but at the same time it hurts the players ability to have empathy for Cocoon and the events going on. When your party starts to talk about "Let's save Cocoon" I keep asking why? I only got to see the ugly side of Cocoon and personally I feel the place does deserve to be destroyed. I had no emotional attachment to the world, and I blame this on the fact that I never really got a chance to see the softer side of Cocoon. Your party has but the player never gets to experience it and I feel it hurts the story overall.

I can understand what you are getting at that the lack of proper towns and NPC's was planned for story purposes, but I definetly have to say after playing the game, it was a very flawed and not well implemented idea.