As you wrote, there is no better time than now to break backwards compatibility for a good of a project. With a longer support of version 3 there will be no problem with it. The benefits in the future will be notable.
As far as I can understand other decisions, I think all of them are the best possible. In a more abstracted way, the speed, simplicity and flexibility are the pillars of CoreIgniter from the beginning. That is why I am using it. Thank you for your work and good luck with a new version. :-)
