I can’t say the story started with abandoning Quagga, it rather ended with it as without fully functional VC releases fork is the only way to keep the product alive. It started way earlier, and there are many things we think should be handled in different way, including community patch inclusion and other stuff.
Why Quagga was replaced with a proprietary product and why they are trying to hide it now is more of a question for management. I don’t know enough details and not sure which details I can speak about even.
Not sure if TFTP server installed by default is a good idea. I see no reason not to include it optional packages though. Addon repository is planned, but we are not yet sure how to make it equally convinient for VyOS and EdgeOS users. Chances are there will be need for two repos, as some packages that will be in VyOS by default may not be in EdgeOS at that point.
Also, consider filing bugs/enhancement requests for your suggestions in our bugtracker: http://bugzilla.vyos.net/.