"* the house is not very child friendly -there are cream carpets and lots of nick nacks and breakable things around to be broken/swallowed"
Invest in a carpet cleaner and persuade your FIL to move the dust gatherers nicknacks higher/away.
" I don't like the house or feel at home there - it is dark, the decor is very old fashioned and not very practical. We would be limited in what we could change."
You may grow to like it. As for the decor, it's a situation many (including myself) face when we can't afford to change it. I've lived here 15 years, I still haven't got to the horrible 70's bathroom. It becomes invisible with time.
"* I would be moving from a place I love where I have just started to make good friends to a place where I don't know anyone (the commute between the two places is 40 mins each way so I can't see myself doing it more than a few times a month)"
Could you look at it with 'I'd have had to move when we bought' eyes?
"* ds1 has friends here he would miss and would lose his nursery place (although he has yet to start)."
He is very young and will make new friends.
"*living with extended family even part time is hard. The kids might start to annoy his dad in big doses."
Absolutely. Can you discuss this in advance with your FIL, plan strategies for when it happens?
"*there is a strong possibility moving there will piss DH's sister off and been seen as unfair by her."
That is her problem and not yours. A sensible SIL would appreciate the un-ideallness of the situation.
It COULD work, but would involve compromise and effort on everyone's part (your, DH, FIL). The second sitting room could help enormously. That one could be child-friendly and for daytime use, with the nicknack-bedecked room used when the DC are in bed.