I also went to the Philippines in February 2022 for 1 month and I can beg to differ about the experience. The border reopened on February 10th for foreign tourists so you probably entered before it as you might be already married (before the reopening, only foreigners married to Filipino nationals can enter with proper paperwork and quarantine). However, I also did have to pay 200$ to get a 24h RT-PCR test at this time and I'm fully vaccinated. Fortunately, I will travel back in 11 days and none of those requirements apply anymore as I have a booster too which removes the testing requirement. I could have met my now wife in a third country but we decided not to due to unneeded expenses and hassles. Those are our personal choices and in the end, we met again and married last march.Are you able to offer us a worldwide comparison of vaccine-related border controls? Can you identify Canada as the worst or among the worst of all countries in the world? I see your comment as just plain silly. If you think Canada makes it tough, I can find worse. I went to the Philippines for 2 months in February. Their law required full vaccination. To get in, one also had to provide a negative RT-PCR test done 48-72 hours before flight. Very few labs in Canada were processing those tests in that short a time. I had to pay $350 for results guaranteed in 24 hours. Then, I had to quarantine in the Philippines for a week anyway. I had to report first to a center where I was examined, required to fill out questionnaires and be photographed. Most SE Asia countries were the same at the time. I refrained from calling the Phils government insane. It was a case of an elected government doing what it though appropriate.
I won't even comment on the notion of sponsoring someone you have never met as a conjugal partner. I would hope Canada would not permit such a thing. That would be an insanely lax attitude to granting permanent residence.
As others have said, is it simply a matter of her not wanting vaccine? If so, tell her to bloody well get vaccinated. Many who are not enthusiastic about being vaccinated have gone ahead and done it in order to travel, like it or not. Or is there a medical reason why she cannot? Even then, I cannot see Canada granting her any kind of exemption. And are you barred from going to see her in her country?
For the OP, I agree that without a physical meeting, the application is guaranteed to be rejected and I hardly find any obstacles because if there is a will, there is a possibility. Personal choices aren’t an obstacle for IRCC whether it is legitimate or not.