I love the mouse mode. It makes this game much more fun and easy to replay. You don't have to think as much or let user error kill your runs.
Have you considered giving manual mode a slight speed bonus to encourage people to use it? Making your minions move quicker while on it.
It rewards the difficulty of aiming the snake, and the mouse mode allows perfect precision.
This is a great game, and I'm looking forward to the updates. It provides a very fun experience.