I agree with you about Manila; It would be great to be able to fly non-stop, and without the unecessary hassle of getting a connecting flight and wondering around in the Middle East aimlessly:
If BA were to reinstate the Manila route, I would understand their reasons to not travel via Hong Kong; there are far too many low cost carriers in the region which BA cannot compete with, offering fares for a fraction of the price down to Manila. However, they would probably benefit from extending their Dubai route onto Manila, as the only airline out of Dubai into Manila is Emirates which BA would compete with, and flights are often overbooked both ways meaning that passengers would benefit from anoth choice or carrier. As there are millions of Filipinos in The Middle East, seats would always sell.
Another choice could be to go via Delhi like they did years ago, but as Philippine Airlines has recently started a Manila-Delhi route, it may not prove to be as viable.
The Kuala Lumpur and Seoul routes may have become unpopular owing to the fact that Korean Air and Malaysian Airlines fly non stop, whereas BA had to fuel via Hong Kong. As Philippine Airlines hasn’t flown to London since 1998, there is no direct competition for the route. Bring back BA to Manila!