Not quite. I was one of the UK negotiators on the CAP, though I confess my memory isn’t what it used to be!
In order to be eligible for the basic payment scheme, I think you had to leave 7% of your land in ecological focus areas. IIRC some of the things you describe could be used for EFAs, provided your country had good enough land mapping. Ponds, I think not, because why would you be eligible for a farming subsidy on a pond?
The move to land based subsidy instead of production based subsidy was UK policy. That was to get rid of butter mountains, wine lakes etc, which artificially kept prices high for consumers while still favouring large producers over small.
Again, this was UK policy. The subsidy involved for very small farms could be more than the administrative cost of issuing the subsidy. It was actually up to member states to set the cutoff point. Malta chose 0.3 hectares, paying out 30 euros as a minimum payment, Austria chose 1.5 ha, Sweden 4 ha...
My comment, not UK policy, for thought - If you only have 5 hectares, are you really a farmer? If that was covered in wheat, you’d have grown on average about 40 tonnes of wheat a year (probably less, because that average is brought up by big farms, but for ease of figures...). That would have brought income - not profit - of £6000 a year assuming a very generous price of £150 per tonne. Tough to live on even with an extra grand in subsidy.
Yeah, that’s not good. While in, the UK managed to get changes to CAP to make it more environmentally friendly. Now it will be Sweden leading the charge, with 27 fewer votes in Council to rely on.
This was the sort of thing the UK was trying to do in the EU - moving payments from Pillar 1 (direct payments) to Pillar 2 (environmental payments), as well as reducing the overall percentage of EU money going to the CAP. We had some success, but progress was slow.
You might be interested to know the Agriculture Bill you referred to fell in 2019 due to the election, but a similar one passed 2 months ago, the Agriculture Act 2020. I haven’t read it, as I don’t do agriculture any more.