"Re pilot suicide- would exhausting the fuel supply mean that the plane was more likely to sink intact if it was put down in the ocean? Could that explain the flying around for hours?"
Not really sure what you mean? Do you mean 'is a plane that's out of fuel more likely to sink?' No, is the answer to that question but I'm not sure if that is you're question?
"Re transponders- is it possible that another transponder was taken aboard, and could this be set up with details of a different flight"
It's theoretically possible but the chances are very, very remote. The transponders are complicated bits of avionics kit that require very specialist knowledge to modify to change the identity of an aeroplane. It could be done if you had somebody in the maintenance part of Malaysian Airlines willing to help. i think it's very unlikely unless it's a 'terror cell' that's been in the airline for a long time.
"Could the plane be 'cloaked' by pretending to be a legitimate flight thus not raising concerns for ATC in other countries as it flew through them? Possibly a bit far fetched."
If you'd managed to get a specialist t change the transponders then it's theoretically possible but very unlikely. It's not that farfetched if you're a well organised group with help on the ground and in the air but I still think it's a very remote possibility.