In his column for The Daily Telegraph, the former opener said he has enough respect for Flintoff but there could be simply no logic behind entrusting the captaincy to the youngster, who was far from being fully fit.
''It is time to ask questions about the appointment of Andrew Flintoff as captain. Don't get me wrong, I have a lot of respect for Freddie. He is as keen as mustard - a great lad who is not a whinger or a quitter and would never make any excuses.
But you have to wonder whether it was wise to give the captaincy to a guy who had just had three months off with an ankle injury and had no discernible form with bat or ball,'' Boycott said.
''It reminds me of the scenario when Ian Botham was made England captain in 1980. He had to face Clive Lloyd's West Indians - the toughest and best team ever to grace Test cricket. And although he was an ebullient all-rounder with the makings of greatness, his career was still embryonic, and he was afflicted by back trouble. It was too much, too soon, just as it has been for Flintoff,'' he explained.
Boycott felt Flintoff erred on quite a few occasions in the series.
''If Flintoff had been leading a well-prepared team against lesser opposition, he might have been able to find some form and impose himself on the captaincy. But there have been too many mistakes and too many problems. Some of the cock-ups have even been self-inflicted, like the decision to bat first in this match.
''The game started under the kind of overcast skies that should have favoured England's bowlers. You rarely, if ever, get a chance to play on a pitch as damp as this one in Australia. And when you have been struggling to take 20 wickets, it seemed like madness to pass up such a golden opportunity,'' he argued.
''If I had been opening the innings for England, and my captain had asked me to take strike on that first morning, I would have tried to knock some sense into him with my bat,'' said the inimitable cricketer-turned-commentator.
''Perhaps Flintoff was thinking about Perth, where England bowled Australia out and still lost the match. Or perhaps he was wary of Shane Warne bowling last. But either way this was a horrible howler, and that is not hindsight. I said so at the time on radio,'' he added.
''Any team are only as good as the sum of all the parts. And a number of the players haven't functioned. England play four seamers and only two have been bowling well -- (Matthew) Hoggard and Flintoff,'' he said.
Still sympathising with the England captain, Boycott said, ''Flintoff has made some mistakes in this match and hopefully he will learn from them. But I don't envy him his job. This is an inexperienced captain, carrying an injury and going into battle with pop-guns against cannons.
''The hard truth is that, barring rain or a fluke, he will end up as only the second England captain to lose 5-0 against Australia,' he added.
Another former captain, Mike Gatting, also lambasted the side, which is trailing 0-4 with the prospect of a whitewash staring at the face.
''It started off reasonably - but it's getting worse. We haven't kept our discipline, and against a side like Australia you have got to keep your discipline,'' Gatting, the last captain to lead a winning England side down under, told BBC Radio Five Live.
The former captain felt England's bowling at the MCG was ''horrible'' and the fielding was ''poor''.
''All we seemed to do was try to bounce out number 10 and 11. It was ridiculous,'' he said.
Referring to England bowling plans which was leaked to the Australian media, Gatting said, ''Whatever the next sheet of paper they put up is, I hope it says 'let's get the basics right first'.'' Gatting, however, insists that England were unlucky to be 3-0 down after the Perth Test but now sport the look of a thoroughly beaten side.
''They shouldn't have lost in Adelaide and they fought hard in Perth - but here there was a resignation, almost. You can't say they weren't trying, but once you are on the end of a hiding it is not a nice place to play cricket.
''They have really got to try to pick themselves up if they are to get anything out of Sydney. If there is any incentive it is not to lose 5-0,'' Gatting added.