I was almost in your shoes a few years ago with my school choice. We were pretty much equidistant from 2 different schools, one being our defined catchment school, and we were very much torn at the time as to which one to choose.
School 1: Not our catchment school. Single form intake (30 admissions). Preferred choice of many local families, and perceived as one of the best schools in the local area. Most of my extended circle of friends sent their children here (and therefore it would be the school for most my DS's friendship group at the time). The local childcare setting could guarantee pick-up from the school, which we needed as working full time with no local support.
School 2: Catchment school. Small intake (12 pupils). Didn't know anyone with children attending this school and didn't know much about its reputation other than it having a significant number of SEN children. The local childcare setting could not at the time of application guarantee whether they would be able to pick-up from this school as they didn't at that point in time, and would only commit if there was demand for it.
I visited both schools, and both were great, but I was surprised that I got a much better vibe about school 2 during the visit - much more welcoming, the children seemed much better behaved, and happy and confident to interact with visitors. So when it came to the application process I was torn, and ended up putting school 1 as first choice and school 2 as 2nd, primarily due to the need for the after-school childcare.
We didn't get a place at school 1 - it was oversubscribed that year for the first time in years, so we accepted the place at our second choice....and haven't looked back. I'm so glad that the choice was made for us - we now have 2 children at the school and they are both thriving there. It's a very mixed (albeit small) intake, which means that my two are mixing with children of all abilities and social backgrounds which I believe will set them up well for life in general. Also because of the relatively high level of SEN in the school - there is excellent support structure in place in terms of both staff, and identifying individual children's needs.
Meanwhile I often hear parents who are unhappy with school 1 - not sure if this is actually the case or whether it's just high expectations by parents.
My recommendation would be whatever the outcome, embrace the school and don't think about "what could have been"- it sounds as though your second choice is still a very good school anyway.