Honda city is good choice if fuel economy is the concern.
You need to do little search and I believe you can buy Honda city with manual gear from 2006-2010 models depending on condition.
Its nice car for city drive and even for long routes also. And you will enjoy it a lot.
Suggestion 1: Before driving make sure its cooling system is all OK and thermostate valve is installed and working. Otherwise it may have over heat issues.
Suggestion 2: When buying used vehicle, always keep 1-2 lakh spare in hand to spend on it. Because apparently these vehicles may look good but after buying when we bring them in our daily drive routine, then we know that how many works need to be done like suspension, tires, cooling system, tuning, fluids change, etc.