Mmmmm. Apples and pears sir.
I would probably use LHR for your specific flights and the fact you had a transfer.... but the point of city is the fact that it is an "airport" in the old fashioned sense of the word....... you can still turn up 35 mins before the flight, through security and away........ not a glorified waiting room..... which is what many airports have become.....
~ I use LCY regularly for point to point and the BACITYFLYER ERJ 195SR is a superb aircraft, quiet, comfortable and new.... few children or infrequent flyers clog the airport up.... and little point in paying for the CE product, either.
Interestingly I yesterday booked AMS-LON-ABZ via LHR in CE in preference to LCY..... for similar reasons, more flights, lounge etc....but had I just been going AMS to London I would have used LCY and flown in Y.