Yoghurt Bagels - What's the best flour for a healthy breakfast?

I was getting bored of eating yoghurt so I decided to make Skyr Yoghurt Bagels with a smoked salmon filling. I ended up using way more self rising flour than the recipe suggested.

I've been trying new breakfasts to lower my sugar spike and be healthier, but I think the amount of self raising flour I used for these bagels defeats that.

Please can you suggest a better flour substitute, or are these just a bad and unhealthy breakfast decision?