How on earth to decide which school?

[mirandaspanda]

This is my first post and it's one made out of some bemusement. I really thought someone who's already been through the secondary school process would not struggle this much when it comes to the second child.
Background: we live in a rural location, a mile from the local village where the primary school is. Primary school was something of a disaster for unacademic DS1, whose behaviour (mostly associated with immaturity and two years R and Y1 with a teacher who shouted at him daily) very much soured relations with the school where DD and DS2 remain.
We are in catchment for an outstanding, yet huge secondary school, which DS1 currently attends. At the time DS1's decision was made, there was a effectively choice of three schools- the other two being a faith school that is a good hour on the bus away, or a more local school with a RI Ofsted, which nobody in his year group chose. It should be noted that logistics for DS1's school involve a mile bike ride and a 7 mile bus journey, which despite being catchment, we have to pay for and is very expensive. (Long story)
DS1 chose his school with our agreement. So far, the school has been a mixed bag. He's actually discovered he's not as stupid as the primary school told him. (I admit to being bitter about them telling him there was no point in worrying about SATS as he wouldn't pass any of them - this was the Friday before the real tests.) He has made it into one top set but languishes towards the bottom for maths (he failed the SAT by 2 marks apparently.) His behaviour has been improving but he remains disorganised and attention is a real issue. There is a question of whether there is a deeper issue here but that's for another thread.
The teachers have been helpful and motivated - we have had long discussions if there has been an issue and they have been responsive. I know of several teachers who think it is an excellent school to teach at, and am aware of 3 through personal contact who have left jobs in the independent sector to pursue a career there. So I do not doubt the quality of the staff in general.

Fast forward to year 6 DD. It would seem obvious to send her to the same school at DS - it's outstanding and its offers most things - extensive sports, arts etc and is academic with very good "value add" results.
The faith school is a distant possibility - theoretically we should get a place coming from a feeder faith school (and being regular Church goers), however, we are a long way from the school and lots of people have discovered that all you have to do is get a child baptised (and never show up again.) This means that we are now unlikely to get a place. The third school offers no benefit (RI Ofsted, 7 miles in the wrong direction from other school, don't know anyone there), other than a free bus.
However, DD is quite concerned about the size of DS1's secondary school - it is a 10 form entry. She is bright, extremely sporty but needs her confidence bolstering. She has always felt that her time at primary school has been shadowed by DS1 and his behaviour. She was bullied badly in year 4 - something the school handled badly. It resulted in bullying behaviour towards us as parents, which DD was aware of through the meetings we had about it, where she was present. OH and I could not agree on whether or not to move her (even after the child causing the issue left) - partly as DS 2 was doing well there, and partly due to threats made to me by the school. (Another story).
So here we are with DD being not entirely happy at her current school. She's wary of the staff and has a general feeling they don't like her or respect our family. This is making any secondary transition rockier.
Most of her peer group will go to DS1's school. She has told us that's she's not sure of it - clearly we will go to the open evening. I would expect some nervousness about the secondary school transition but I think some her reluctance is to be in the same school as DS1 because she is concerned the teachers will treat her differently because of DS1, based on her experience of Primary. Therefore she has been asking us about different schools.
We could afford to send her (and DS1) to an independent school. But there is no obvious option - certainly not one, which would suit both children (and DS2 in the future). The schools are a long way away (7am bus and 5pm return assuming no clubs with logistical difficulty for jobs). I am ware the schools are either very academic (Cambridge) or not so academic but don't offer much more than DS1's school, which has an excellent extra-curricular programme.
The one benefit would be if they could offer DD 5 days a week of her chosen sport (swimming) - given we spend hours in the car ferrying to and from after school as it is and it takes up a huge amount of family time. So far, one of the schools has indicated it may be able to tailor a programme for her, but I am not convinced that this would be better than her current club, which has sent people to county and National training. I suppose my reluctance is also that this would entail additional drop offs and pick ups 15 miles in the wrong direction so probably not much of a benefit to increasing family time.
I am not expecting any realistic answers to this thread but I suppose I am looking for reassurance and perhaps some insight from people who have sent children to different schools, or considered doing so but decided not to.
Part of me thinks if you can afford independent education, you should go for it. There must be a good reason why thousands of families make the sacrifices to send their children to fee-paying schools. There are smaller classes for example, more individual attention, better facilities etc. Has anyone decided against independent education?
I have just re-read the marathon post above - you deserve a medal if you got this far. Upon reflection, my gut feel is DD should probably go to the same school as DS1 and we could move her if it failed to work out. Advice gratefully received.