It is the fact that some items/features are only possible for you to get when you are part of a faction.
Now don't get me wrong, it is understandable for most rewards to be only possible for that faction.

However, for example, you have to join the Companions to get a part of the firebreath shout and you have to join the college to get a Dragon Priest mask.

This is a bit annoying because warriors might want to gather all masks to get Konahrik, which is very handy for warriors. But not join the college because they don't want to end up as Arch-Mage without having an impressive skill in magic.

And a mage or battlemage Dragonborn might want to get all shouts, but does not want to join a guild focused on warriors who dislike magic.

You understand what I mean here?

I was hoping to make a battlemage warrior using frost magic and a blade, I don't mind her joining the college, but I am not sure if she makes a fit for the Companions. However, I want to gather all shouts for her, even if it is firebreath and she uses frost magic.

The Guilds are poorly done,It's a fact can't get around it....