It depends who you ask, but in my opinion, a 5-speed manual is better. It actually feels like you're driving the car with a 5-speed, as opposed to just going along for the ride. You can also get better fuel economy out of a 5-speed since you can change gears earlier, and you can generally get better performance as you can rev it as high as you want.
However, if you experience a lot of heavy traffic daily, such as on the way to work, then an automatic is much more suitable. If you're after performance then the 5-speed manual is the way to go.
My father had a 5-speed manual Echo T-Sport, but ended up selling it and buying a 4-speed automatic Vitz RS instead as he experiences a lot of traffic on the way to work every day (and he's getting lazy in his old age ). Personally, I've owned manuals all my life, and can't see that changing anytime soon