Am I the only one who finds this a bit off putting? If I choose that my character should not be a part of certain factions/guilds it results in me basically forfeiting certain shout words. Wondering why they would add that element of design into the game.

It's because the developers thought it would be cool, and they lost sight of the concept of roleplaying (an increasing problem in this series.)

Your freedom is an illusion~

But yeah, I hated this in the game, and it's not only limited to shouts. Take the Gauldur Amulet for example, or if you want Konahrik's mask...

At least with the Dark Brotherhood you could either join them or destroy them to gain the word for the Marked for Death shout

I created a mod awhile back that allows you gain Bend Will shout without going through the DB main quest. It wasn't well received though and people called it cheating. Wasn't much point to do it for the other quest locked shouts.

You're in the minority.