Very interesting points! I admit that my interpretation is very much coloured by the excellent introduction to the Oxford World Classics edition of the Histories written by P.J. Rhodes. I believe Thucydides was far too cynical to buy into the propaganda, and was less than wholly enthusiastic about the way Athens conducted the war, as the placing of the Melian Dialogue directly before the Sicilian Expedition showed. The prominence of Pericles' funeral oration certainly showed that he did not lack pride in his native polis.

The animosity towards Cleon is definitely related to the stark contrast with Pericles, and there's no doubt Thucydides mourned Pericles' death. On the other hand the capture of the Spartans on Sphacteria was due to Cleon, whether it was up to luck or not, and although his attempt on Amphipolis was unsuccessful he paid with his life. These two events largely ended the first phase of the war on grounds more or less favourable to the Athenians, so I would say Cleon doesn't deserve the extra ire directed at him by Thucydides, Athens certainly had worse generals.

Speaking of which, the portrayal of Alcibiades is indeed also very negative (and in my opinion well deserved). Whether or not the presence of Alcibiades himself in the expedition would have changed the outcome is an open question, but his removal was due to political intrigue (democratic politics is always messy) and hardly his own fault. Anyway he carries the family curse so can't be too harsh on him :).

The point of your original post was that historians biases colour our own views. I think the fact that we spent all this effort here trying to guess what Thucydides might or might not have felt about certain things is in itself a testament of the neutrality of his work. It is very difficult to paint him as a partisan purely from the text in his own works, so in this case I believe Thucydides is actually a counterexample to the original argument.