Looking for somewhat of a guideline on what to do, beat both Oblivion and Skyrim so I'm a little disappointed thus far at the discombobulated story line, any help would be greatly appreciated. Thank you

play 1-50 once through and do it however you want, then go back and do it a second time with another char and you'll get what's going on much better.
But basically:
Main quest is about vanquishing Molag Bal
Mages/Fighters guild lines are about Eyvea and the Mortuum Vivicus (excuse the spelling, I forgot how to spell them exactly)
Quests in territories are about the events there, some of which involve Molag/the Planemeld, some of which involve other alliances and the current war, some of which are internal affairs.

Feel free to pm me other questions if you have them.

Ah thank you very much, currently level 30 on my first run thru it's not terrible just not as grasping as the past few have been. Appreciate the tip!