So let me just try once again to summarize how the PhD stream can exist after Express Entry (assuming you don't have nomination from a province or a job offer yet). The following are my interpretations of what has been posted on the CIC website (I'm not a legal expert, so take it as it is):
1. You need to satisfy ALL of the requirements for the PhD stream (including the minimum work requirements, language skills, educational credential, 67 points or above)
2. Once you satisfy ALL of the requirements of the PhD stream, you can then get onto the Express Entry pool for consideration, to be ranked against other candidates)
3. You will then be assigned points under the new CRS (comprehensive ranking system), where, WITHOUT a job offer or a nomination from a province, you can only max out at 600 (whereas with a job offer or a PNP, you can max out at 1200)
4. Now, out of those without job offers and without PNP, they will be ranked against each other, and CIC will only invite those with the highest points, irrespective of when they enter the pool (so it's no longer based on first-come-first-serve)
5. If you are among the top performers when it comes to the number of points, you will then be invited to apply for PR
So for those who can only qualify for PhD stream next year, do not lose hope yet. Until we know for sure whether the PhD stream will be closed, you may still have a chance. Obviously if you can qualify this year, you are advised to apply the soonest you can.