Well since I installed tons of mods from day one of playing, I augmented my Skyrim to be much better to begin with. I suppose that stock Skyrim is pretty bland, but I have not played it stock so I wouldn't know.
Regarding the main quest, I only had two problems with it, the fact that the Blades want you to kill Paarthunax and you have to pick a side, and that the battle with Alduin was far too short and simple. Sovngarde was beautiful, but it lacked content.
Regarding faction quests, I found the Companion quest line to be quiet enjoyable. It was the first thing I did once getting to Whiterun and at a low level, the reclamation of Wuuthrad and the werewolf thing was very interesting to do. I sided with the Stormcloaks (haughty high elves piss me off) and due to the civil war mod, the battles were much grander.
As for the combat system, all I see are improvements. I remember the days of clicking rapidly and hoping that my attacks happened to hit. I love Skyrim's system so much more. Sword and shield has never been done better in a game in my opinion.
Regarding "no soul", grab a few Immersion mods. I removed all quest markers and changed the map around. Greatly improves immersion. I once spent at least five hours playing just out west of Whiterun with a bow and iron arrows and hunted the wildlife. It was pure time wasting and no quests were completed and I didn't make any money, but I was having a blast.
