To be fair, the delays attributable to baggage handling and offloading have reduced considerably in the last year or two. Most delays I have experienced lately are from the ridiculous flow control and slot allocation procedures. I am sure that the ATC guys and girls are embarrassed by the whole thing too but it is something that can only be solved at the highest level in the U.A.E.
In the intelligent world the flight dispatch appliy for a slot in advance based on ETD. In DXB at present, the slot is awarded as flow control sees fit and the crew work towards that end with a reasonable allowance for unforeseen delays. The current UAE system of only awarding a slot once the flight is fully ready for start is plainly stupid. Add to that a two minute window restriction the problem becomes compounded.
I am not blaming the lads and lasses at Dubai ATC (if you are reading this) because I know that you are just working within your restrictive remit. It would be helpful however if you were to give an estimated expected delay time when transmitting the clearance. This would prevent a lot of unnecessary transmissions and give the pilots some idea of the delay to be expected.