It sounds like you're saying the souls are almost functioning like ammo for the shouts, which would be really disappointing.
Well why else would you gather the souls.
There are 20 shouts, so unless there are actually far fewer dragons and everytime you collect 3 souls of a certain type you learn a new shout then how else would they work?
Well you could need, 10 to learn teh first, the say 25 to learn the second, then 100 to learn the next, But that would eb even more tedious.
Yes the ammo idea sounds bad, but I could defintely seeing it work, if younger, Juvenile dragons, and hatchling, up to Young advlts are as common as they seem to be, Which is uncommon but not liek most Fantasy universes where any Dragon is completely rare.
Hopefully we all enjoy the system that Beth comes up with, of course some wont like it but I expect that it should work out in the end.