I've only had me Yaris for a week and haven't even reached 100 kms on the meter yet, but the centre console is growing on me.
Like you, I was also not fond of the console in the centre, especially since I have glasses and want to be able to see the speed I'm doing!
In Aus, the Yaris hatch has the digital dipslay, whereas the sedan has the traditional analogue. Why my first impressions were that the digital console was pretty wiz-bang, I feel the analogue does grow on you and portrays a more sophisticated look especially when the cabin is dark at night - if you care about such things. It really comes down to individual taste I guess.
Back to your concern about the console being in the centre, while it seems counterproductive in theory, I think the reason behind it is that the extra distance between your eyes and the console may mean less work for your eyes when moving your focus from the road to the instrument panel and back - well, I can't see any other reason for it!
One benefit of the console being centred is that the driver's field of vision is even greater as there is no console directly in front - is this convincing?