Having done a dozen or so T5 to T3 and vice versa transfers in the last couple of years, I have not really had many problems; I do however try to schedule quite a bit of margin between flights.
I do however agree though it is not ideal, and cannot understand why BA, the dominant operater at LHR, did not force HAL to complete the T5 project (full size T5C plus T5D and T5E) before they embarked on T2 which offers BA not benefit at all. This would have allowed BA to operate under one roof, surely a commercial benefit for BA.