Unless you requested the re-route (and as long as you didn't collect miles on SQ as well), you should get the Avios and TP for the flights that were sold and ticketed, regardless of what you ended up flying. I accepted a request at check-in from QR earlier this year to fly LHR-KUL direct on MH rather than LHR-DOH-KUL on QR. At first I was only credited with 140 TP and the MH flight Avios, but after a call to EC, they reinstated the extra 140 TP and extra Avios from the original flights. Got to KUL 4 hours earlier as well...It can take a while though, if the ticketed flights were not BA, as they have to go through the other airline.

Agree with you about BA vs SQ (depending on the aircraft), but I'm not very tall (or wide), so BA does me fine. I do however like the fact on SQ that I can put the TP and miles on VS, but still get credit towards PPS status on SQ.