The dragons are invading Skyrim for a reason, so they are going in full strength.
So what if they operate like that? Nobody is talking of them being special or anything of the sort. What part of DRAGONS INVADING TAMRIEL is so hard to grasp?
They want to destroy the world, find out there's one last Dragonborn roaming the place...and they are gonna come two at a time every 30 hours of gameplay?
So? That doesn't mean that there is going to be an infinite number of them, which is the point I'm arguing.
Typical fantasy lore is that dragons mature to from babies to advlts to ancient dragons over many thousands of years. And AFAIK females do not lay tons of eggs.
I would be very disappointed if dragons became such a regular occurrence that 1) I would just shrug my shoulders at the sight, 2) I could choose to ignore it and not worry about getting its soul because I knew I'd have as many chances as I would need to stock up.
I really think there should a good number of dragons across the world, but the number should ultimately be limited. If you're concerned that the story might suffer if too many of the dragons are killed "prematurely", then don't have all of them accessible right away.