A new system for MPs' expenses clearly had to be devised by an independent body, not cooked up by a Westminster establishment which fought so hard to prevent claims being disclosed under the Freedom of Information Act. That would not have carried any credibility with a sceptical public.

At first glance, the Committee on Standards in Public Life has proposed some sensible reforms and its chairman Sir Christopher Kelly presented its report confidently.

The reaction in the Commons was muted. MPs hate the medicine Sir Christopher has prescribed but know they must swallow it. Voters would not understand if they refused to. That is why party leaders jostled to embrace the Kelly report.

On closer scrutiny, some of the MPs' deep private misgivings are justified. The sweeping changes will transform the lives of our elected representatives. This matters because they might adversely affect the calibre of future MPs.

Sir Christopher insisted his proposals "recognise the unique circumstances of an MP's life". Yet it is an open question whether he really understands the lives they lead.

There is a strong case that the allowances system should help MPs maintain two homes. That will become harder when support for mortgage interest is banned – unless people enter Parliament with money in the bank.

Some MPs move their families to London to keep them together. One woman minister, whose young children live in the capital during the week and her constituency at the weekend, said the changes would mean she would no longer see them most weekdays as she will have to commute from her constituency.

Juggling work and families will become harder under the changes, and could deter women with school-age children from entering politics – bad news for a House which has only 126 women among 646 MPs.

Members who make their main home in London may spend less time in their constituencies, which would hardly close the gap between politicians and public. Many MPs have become super councillors or social workers, presumably because they judge their voters want such a service.

The changes will leave MPs worse-off financially, encouraging some to take second or third jobs. Do we want to return to the era in which MPs worked as lawyers or in the City in the morning and tipped up at the Commons in the late afternoon? What about those MPs who would not have that option? Today the public seem to demand full-time MPs, and new rules that shine a welcome light on their outside earnings act as a deterrent to taking up other jobs.

The eventual ban on MPs employing their relatives may look like a clean-up measure but will increase the financial pressure on them. Despite the shocking case of Derek Conway, who employed his two sons when they were full-time university students, there have been no expenses scandals involving MPs' wives. Most appear to provide very good value to the taxpayer.

Sir Christopher insisted that his reforms would not deter people from relatively modest backgrounds from entering Parliament. Many MPs think otherwise.

He was right to argue that a generous and lax system of allowances had become a thinly disguised substitute for pay. Indeed, successive governments since the 1970s have encouraged this because of the political difficulty of approving a big pay rise for MPs.

There is never a good time for such an increase. Arguably, a recession is not one. Yet with a new expenses regime taking effect after next year's general election, an opportunity was missed yesterday.

Sir Christopher said MPs' pay and expenses should be treated separately, but made no recommendation on salary levels. He should have done. The current salary of £64,766 will sound generous to many voters, but the Kelly report should have coupled lower allowances with a generous one-off pay rise so that people who could earn a lot more elsewhere are not deterred from a career in politics.

How much less will MPs receive?

£4,600

A £25-a-day "subsistence allowance" for food when staying away from main home scrapped.

£24,000

Some MPs living within "reasonable commuting distance" from Westminster will lose their right to the second home allowance. Expected to include around 66 MPs.

£10,000

Communications allowance, designed to pay for MPs' websites and leaflets to their constituents, scrapped.