Mostly because of geography. There was a time when that area of Anatolia did have a major city - Troy. At its height, in the Late Bronze Age, Troy was larger than any polis in Mycenaean Greece. Most importantly, it had a large and well protected port as well as a ship portage way that gave ships traveling north a side entry that bypassed the prevailing contrary winds that came out of the straits. The port also gave great access to the fertile plains of the Troad which in that era matched in area any region on the other side of the Aegean. But by the Classical period, the port had silted in (much due to the effect of the expansion of domestic sheep herding causing deforestation and subsequent landslides). A minor port had developed just a few miles north of modern Canakkale, at Abydos, but it was small and not very well protected. The Dardanelles Strait acts like a gigantic Bernoulli constriction and funnels the wind such that navigation can always be expected to be challenging at best. Once the Scamander had silted in the port at Troy, there were no good ports left in the area (a situation that exists to this day). Canakkale itself is on land that didn't even exist in the Classical period. All the land that the city sits on today has silted in over the past couple thousand years. In the Classical period, Abydos was the closest point to the Gallipoli peninsula. That's why Xerxes built his bridge from there to Sestos on the other side of the strait. Xerxes' trouble in getting his army from Sestos up the peninsula also explains why that end of the straits didn't become a major roadway. The peninsula is very mountainous and unforgiving, making a matching port there unappealing, and that's before we even talk about how the geography has never made a major port on the peninsula side even possible.

The Bosporus, on the other hand, has none of these drawbacks. It is much shorter than the Dardanelles, so it doesn't act nearly as much like a Bernoulli constriction, and certainly not for as long a distance. The Golden Horn was and is an excellent port at the end of the strait (much like Troy's harbor was in the Late Bronze Age before it silted in). In addition, the eastern Anatolian side of the strait has a number of decent protected harbors to allow for plenty of ferry traffic across the strait. And if you are moving an army, or anything else, crossing the Bosporus lands you right into the Thracian plains, not onto the face of a mountain like at Canakkale.

Ultimately, geography is the reason you are looking for as to why Canakkale never developed into a major city to parallel Istanbul.