I don't have much experience with the City since I own a Civic 8th gen with 55,000Km on the clock. My car's fuel filter was replaced at 40,000km. In the Civic, replacing the filter means that the pump too gets replaced. They are both as one unit. I have to admit that following the replacement, there was a noticeable difference in the pickup. I am guessing the design of both cars may be similar in the fuel filter/pump area i.e. the pump and filter are within the same housing. I will tend to agree with what @aamirq is saying about the filter. Price for Civic pump/filter was 9,000.
Do not mess with the injectors - PLEASE. First do the 40,000 km service. If that doesn't restore your car. The second thing to check will be the catalytic converter if you have one on your car. Ask the Honda people to check to see if it is clogged. On the Civic, converter condition can be seen by looking into the hole after removing the O2 sensor. On my, car at about similar mileage to your car, the converter had become so bad that I was not able to reach 130km/h on the motorway. The converter was removed and the reddish deposits on the converter honeycomb removed (scraped) and blown out with compressed air. Following the converter cleanup, my car's performance is back to near new status.
If all the above things don't return your car back to the original performance, then ask the Honda people to investigate further. IMHO, I believe that doing the 40,000Km service should get your car feeling good.