In my humble opinion.. Yes. I feel bottle sacrifices just a little too much for the sake of being a single file distribution. The lack of any (mainstream) templating engine might hinder newcomers, and Flask uses one of the best python templating engines around. I also find Flask's documentation to be more extensive and better laid out. Overall I would recommend Flask if you want to write a full featured website, Bottle if you are looking to write some kind of API layer, or similarly bear bones functionality, and will not require many "batteries included".

You can use Jinja2 with Bottle:

> pip install Jinja2

from bottle import jinja2_template as template