Who instituted Rishon, Sheni, Shelishi etc in the leyning of the Sidrah? When was this done? What are the principles which were applied to determine where the stop should be? One would have thought that the Aliyot would be of about equal length, and that they would coincide with the subject matter, but this is not always the case.
Open up a shulchan aruch, and you'll see the criteria for breaking the Torah portion into readings:
Rule 1: As an absolute requirement, end at a paragraph mark as found in a Torah scroll; or, if you want to end in the middle of a paragraph, not within 3 sentences of the paragraph's end.
Rule 2: Attempt, when reasonably possible, to end on a positive-sounding verse.
Rule 3: That said, attempt, when reasonably possible, to break between topics and not in the middle of something.
Ideally, concern should also be paid to who will be called up for this reading, that it not be something especially derogatory or troubling for them.
That we attempt to divide it in ways that are more or less of equal length makes sense, and is easier on the Torah-reader, but isn't listed per se.
I don't know who put in the current standardized divisions (though there are still some that are debated); they are reasonable recommendations that meet the above criteria. If, for instance, a synagogue wanted to add one (or more?) aliyahs, a reasonably-knowledgable Torah-reader would look at the above rules and make an additional division as suits him.
In some Torah portions the divisions are a bit more conspicuous; for instance, Vayeshev is a rather depressing portion: "they hated Joseph, they wanted to kill him, they sold him down to Egypt, his father mourned, he got thrown in jail, the baker died, Joseph got left in jail." The divisions here try to find any nice-sounding verse, and end on that: "his brothers hated him, but his father held on to the matter." [STOP! SOMETHING NICE-SOUNDING!] "The other brothers wanted to kill him, but Reuben secretly wanted to rescue him." [STOP!] Or in the next portion, this mysterious and sadistic Egyptian viceroy is making the brothers completely miserable, but at one point he offers to make a deal, "because I fear the Lord." [STOP! SOMETHING NICE!]
The whole sordid affair with the Golden Calf is crammed in to two ginormous aliyot given to the Cohen and Levi; the five non-Levites after that get small slivers of the remaining portion. This is to avoid giving any of that sad issue to a non-Levite (whose ancestors likely participated in it).