What determines what we teach and when in Gemara? What are we trying to accomplish during Gemara shiurim? Are we trying to teach skills? Knowledge?
Many schools continue with a general notion of why they teach what they teach, but the details have not been hammered out. Some schools teach for Halacha leMaaseh and therefore teach Masechtot in Moed. Should a teacher be able to decide which perek they are teaching in a masechta? Would we call the first perek of masechet Shabbat Halacha leMaaseh? Should the sugyot being taught be determined beforehand?
Schools teach tefillah, Shabbat, moadim, Kashrut. Should there be a progression?
Other schools emphasize Brisker lomdus. Again, certain perakim lend themselves to better application of Brisker lomdus. Imagine trying to teach the 7th perek of Baba Metzia for lomdus, instead of the numerous other perakim that more easily lend themselves to this style of analysis.
The answer to these questions will depend on what the school's goals are. On a finer level, what are the school's goals for that grade/section? Only when goals are articulated can the appropriate content be selected. The step after articulating the goals of gemara is aligning content and teaching methods to those goals.
For example, if we are teaching for skills then specifying the content would allow for a detailed map of which skills and words appear on each daf. This would guide the current teacher on what to teach and also inform the subsequent year's teacher what skills and words his incoming students have already learned.
If we are teaching toward Brisker lomdus and we are learning the first perek of Kiddushin, so we could list the sugyot on each daf, with critical rishonim, but we would also skip the elaborate discussion on 2B, since the discussion is more focused on semantics.
The challenge with this method is that it does not seem traditional in that it does not mimic the yeshiva experience. That is true. The first question is, is our school yeshiva prep? The school I work at is, and this means that we give our students the skills to succeed in yeshiva, even if the experience is different. High school general studies courses are structured differently than college, even though high school is college prep.
Too many students feel that they are just going through pages of gemara and are not sure why. Having clear goals in each grade explains that.