It's not unrealistic that there are political preferences in Turkey. However, I think that is hard to say. I certainly would not state it in the absolute. Sites that are not connected to the Ottomans, easily excavated and then visible to tourists are naturally rare in Istanbul.

But many of the sites are not Ottoman in origin, and are quite central to the cities archeological portfolio. On the other hand, artifacts (like the ships they discovered during tunnel excavations) are also on display. They are just several layers under the Ottoman Istanbul so when you find them, it's not going to be a whole site you can visit.

Another hint might be that if you go outside of Istanbul, there are a lot of Greek era sites (or even earlier sites) that are "the" highlight of the adjacent region or city. Assos, Ephesus, Troy, many things in Bodrum, Cappadocia and many more. Here, the problem is clearly money. Take Assos. They do what they can, and it's fully excavated. There just don't seem to be the resources to feature it in a more exciting fashion.

Finally, knowing people who are Turkish archeologists, I would say they care about the entire history of the place just as any other archeologist would.

In any case, I also hope there will be (and it seems at times that there is) more resources to excavate, understand and display all the historical sites found in Turkey.

To be clear, I am not Turkish, but I go there often.