I feel that The Ottoman Navy performance becoming worse during the 17th Century onwards despite multiple successful reforms like introducing modern sailing ships and the reform of Selim III, the navy still performed overall badly and rather get defeated easily by its rival's navy like in Çeşme, Sinop, and Navarino Bay. While there's a clear reason on why the army performed poorly at the later 18th century to the reforms of Mahmud II like the civilianization of the Janissaries and the decentralization of the military, i haven't got a clear answer on the navy yet. So why is this?
I am not a historian but I consider myself as a ottoman naval history enthusiast. I hope my answer is helpful.
Prof. Idris Bostan published a great book about this subject (https://books.google.com.tr/books/about/K%C3%BCrekli_ve_yelkenli_Osmanl%C4%B1_gemileri.html?id=1S81AAAACAAJ&redir_esc=y)
Name of the book can be translated as "Ottoman paddle and sailing vessels" and has a lot of picures, letters, infographs , etc. in it. To answer your question these notes can be listed :
1-) Ottoman Navy under Barbarossa and Sultan Suleiman was doing well but Spanish and English began using galleons at the time. Galleons were big and heavy ships and were not performing well in Mediterranean and low winds. That's why ottoman naval engineers decided to stuck with galleys instead of galleons because Mediterranean was their main hinterland and Venetians were their main enemy. Venetians decided to do the same which led the decline of both states because they could not compete with new world exploring. Discovery of the Americas gave advantage to Spain and England where they lacked financial and raw material resources in the following years. According to me this may be one of the most prominent cases of a technology selection shaped the fate of an empire.
2-) During stagnation period , Ottoman elite and high bureaucracy were shaped by bribery and not the skills. Prof. Bostan gives a letter from Sultan as an example where how angry the Sultan Selim III was during a commencing of a ship, it directly sank in the water. That's why he favored french shipbuilder Jean-Baptiste Benoit over Turkish shipbuilders. This led crisis in Turkish shipyards and eventually Benoit had to escape from the Empire. Ottoman sultans were directly managing navy and shipbuilding process. In one directive of the Sultan himself criticizes the geometry of a ship and ordered engineers to build it with a better mathematics[sic.]
3-) Bribery and corruption were wide in military personnel as well. Huge ships were under order of unexperienced admirals who lacked active combat experience. Because of low skill navy staff a special law needed to be prepared which shaped rankings and minimum requirements to lead a ship.