I spend a good deal of time on tracatates Shabat and Eruvin.--The reason was force of circumstances. I had spend the previous two years in Shar Yashuv learning Ketubot and Yevamot. So when in my new yeshiva--the Mir in NY-started learning Ketubot, I felt it was time to start something new. So I did Shabat with a lot of the Tosphot, the Tur Beit Yoseph, Maharsha and Pnei Yehoshua. [I joined the small group that was doing Shabat in those days with my learning partner Hagi Presher who later became a rosh yeshiva in Russia and with Rav Nelkenbaum who is one of the roshei Yeshiva in NY in the Mir.] I did not however finish everything because in those days I was tried to get through the material as fast as I could, but also to understand it. Recently I put some nice ideas about Shabat (link) in my little booklet on Shas that deals with the most fundamental aspects of Shabat מלאכה שאינה צריכה לגופה. At the time I was thinking about these things, I was learning with my learning partner, David Bronson, who had a copy of the Avi Ezri. The fact that he had the Avi Ezri of Rav Shach was very helpful. The main thing about Shabat is the Tosphot in Yoma page 34 or its sister Tosphot in Shabat and Sanhedrin. [Take a look at Rav Shach. The ideas there are astounding in depth and clarity.]
In terms of getting through Shas, I would prefer it if you would do a half a page per day with Tosphot and the Maharasha. Or if you do a whole page, then to still do it with Tosphot and the Maharsha. I think that it is important to get an idea of what is going on in Tosphot in one's early years,- because doing so later is often impossible. This is the reason why the places like Shar Yashuv and the Mir get involved in Tosphot even in the high school years. I did not understand at the time why learning Tosphot was important when I had not even finished Shas once, but now I see the wisdom in the approach of the Litvak [Lithuanian] yeshivas.