I think this is probably the weakest of the Tennant specials - RTD seems to enjoy starting new Doctors with relatively lightweight, farcical instalments. I think that makes sense, as it probably helps the exposition go down, but they remain my least favourite flavour of Who.
I remember reading that Beep the Meep was some kind of legacy character, but avoided spoilers. Nonetheless, I didn't find the big betrayal very surprising.
Resolving the meta-crisis in the first special did surprise me, but it was probably a good decision.
Regarding "The Boss" - do we think that's a mystery for another day? It doesn't really make sense for it to be Sutekh...