Jon,
I shared your views about Percival until I read Farrell. Percival basically is blamed for a lot of thing he was not responsible for, including a lot of interference from the fat cigar smoking guy... It was not just the Western Desert, it was eastern Africa, Syria, and the aid to Russia. London scrapped reinforcing Malaya and Burma (where my British Army idol, William Slim was beaten, saved by the NRA, but never blamed...) several times, despite warnings. Yes he could have done more to train his Indian units, but on the other hand his battalions were constantly milked to create new ones. On top of that he was wedded by Churchill to the concept to defend the naval base and the mass of empty RAF airfield everywhere in the peninsula.
Finally there was the complicated chain of command. He had more or less no authority over Bennett because Bennett styled himself (without authority one must add) as commander of a separate contingent and was willing to cooperate only if more authority was granted to him. Bennett refused subordination to Heath (III Corps commander) and acted only when granted a sort of corps command later on. It was a mess and when given authority over other units Bennett did not prove capable to control them effectively (he had a division HQ after all).
Yes Percival could, and probably in a perfect world, should have cracked hard on Bennett. But Bennett was Australian, London has more or less ignored Australian warnings and just siphoned troops for the ETO/MTO (including Churchill's adventures) so the War Office ordered Percival to stay put. It is worth to note that Wavell did not really improve anything even when sent there.
I will also add that Tom Phillips did a real poor job (messing with air cover, failing to inform Singapore he had been spotted, failing to inform his chief of staff he was changing plans and that air cover should have been re-arranged, then the CO of the Prince made several poor tactical decisions during the actual engagement...), but having gone down with his ships no one is willing to go too hard on him.
Things Percival could have done:
1) replacing Heath when he was showing sings of fatigue, but with whom? Paris was an alternative, but he was fatigued too and he was a brigade commander.
2) scrapping the defense plan and just deny Singapore (but Churchill would have removed him).
3) forcing Bennett to do his job, but it was politically impossible both with London and Canberra.
One issue with Bennett is that his own expectation to lead the AIF was not completely unfounded. Blamey appointment over him has more to do with Australian politics than military competence (incidentally plenty of officers, Australian and American had a poor view of Blamey). Reading Farrell I got the impression that Curtin was unwilling to rein Bennett for a while being afraid of his pre-war relationship with Blamey being put into the spotlight.
I will be wary of Yamashita's comments. He was competent, but also prone to underestimate his adversaries and certainly he had some issues in the campaign including a progressive slip of control over his troops. It is also worth to remember that Yamashita 'buckled' his own estimates and was more or less one month late in taking Singapore. I am also not at all persuaded that the Japanese showed great effectiveness in the campaign. Yes some units performed well, some much less. The three divisions employed were certainly of different quality. Japanese tactical doctrine proved superior in Malaya, no doubt. But on a certain level it was more a case of the Japanese almost unknowingly exploiting weak link in the CW doctrine (that they themselves did not really known).
Conclusion:
in a similar situation even Slim failed, he escaped to India and rose to almost mythical proportions, in large part because Burma debacle was hidden by Singapore. In Percival's situation few would have done better.
I have designed a nice little game on the topic (self promotion bit! It is cheap you can get printed or PDF, it is called Lion of Malaya and it is published by tiny Battle Publishing, you can find it on wargame vault!) and I think to have portrayed a balanced view of the situation. People are always welcome to try to improve on their historical counterparts' performance!
Despite being a great admirer of Japan, and having plenty of Japanese friends I cannot really disagree with your last bits. What happened toward the end of the campaign (hospital murders, the butchering of Malay troops) and after is not going to the credit of the Imperial Japanese Army (understatement!).