Get the 64GB 6s. Don't get me wrong, I love the bigger screen but ample storage is a must have. Most users will struggle with only 16GB, especially after iOS and stock apps eat away a quarter of it.
Absolutely get the 64GB 6S. Like Banker said, these days, 16GB is nothing at all. A few decent sized apps and you won't be able to take/store any more pictures.
I would go with the 64gb iPhone 6s over the 16gb iPhone 6s Plus, I need storage space vs. screen size. Now if you don't need storage space and want that BIG beautiful screen go with the 6s Plus.
No one has really asked whether 16gb will be enough for you! If you usage doesn't require lots of storage and you want the bigger screen, there's your answer.
Don't let other people decide or convince you that you need 64gb or 128gb. Figure out what you realistically need and go from there.
All my ios devices have been 16 gb and that works for me. Pictures I sync to Google photos soo they won't take up so much storage on my phone. Now I have 6 gb left. If 16 gb is enough for you I think you should go for the bigger screen if the size is for you.