Do you think they could make a transitional arrangement for this though? Ie you meet the requirements when applying for the Fiance Visa - new rules come in - you apply for FLR - you are still bound by the rules that were in place when you first applied for the FIance Visa?
Yes, I think they will - that is what the whole 'grandfathering' thing is about.
If you applied for a fiance visa under the old rules, then you were let into the country and allowed on the family visa path based on the current requirements. It wouldn't exactly be fair to suddenly expect you to acquire an extra few thousand pounds of income a few weeks/months later when they just said you were okay with a lower income.
In my experience of changes to visas over the last 5 years, grandfathering is common and usually the rule changes will only affect new applications outside the UK.
For example, they got rid of the Tier 1 General visa in April 2011, however, people who are already living in the UK on a Tier 1 visas are still allowed to apply for a Tier 1 extension when their visa expires, even though technically the visa no longer exists. They can also still apply for ILR after 5 years in the UK on Tier 1.
Similarly with Tier 2 General - the new restrictions on income for ILR will only apply to people who apply for ILR after April 2016... which means that the majority of people who are already in the UK on work permits or Tier 2 visas will still be able to qualify for ILR under the current/old requirements (i.e. only people who got their visas after April 2011 will not reach 5 years in the UK before April 2016).
And not related to immigration, but similar things have occurred in other areas... like when the government introduced top-up fees for university students. They announced the new fees in 2004, but said that the higher fees would only apply to new undergraduates who started university after a certain date (2006/07 academic year)... so anyone already enrolled in university at this time would still only pay the lower fees - my brother was a student from 2004-2008 and he paid the lower fees (just over £1,000 per year) for the entire 4 years.