I played the three games, and I think this one is my favourite. Because the other ones had more of a linear and direct ending but after looking more into the endings of this one, they turned out to be deeper than they seem.
(Contains spoilers!!)
Alright so at first I thought the endings where normal, and didn't have that much depth to them but now to think of it I changed my mind. The "True Ending" might seem like the happy ending... but is it really? I have some theories on how this ending might go. First, everything is fine and they are going to the city, but will they make it? They could easily just get attacked again and there it goes... Or they get to the city and for them to get the cure from Nana.. the process will put Nana's life in danger, something like that..
The second theory is that nothing of that really happened.. I mean when I think about it, Kotaro did fall asleep when you choose to not to listen to Nana, it could all just be a dream, and Kotaro saying "I am not sure if this is a dream or not." it just makes sense..
I like how you didn't call the other ending a "Bad Ending" it's just called "Ending" and you didn't give it a description which makes it more interesting, and opens for more possibilities.
So yeah.. this was long.. and I could just be over thinking stuff. Overall I loved the game :)