Well, I am in the interesting situation of doing both this September!
Both my DC were at the same prep. DS has just left at 13+, DD has just left at 11+.
For DS, staying on for 7 and 8 and going down the CE route was a huge success. Yes, CE is demanding, but they are working with teachers who know them (and their weaknesses) really well. The CE curriculum moves them on in their learning, compared to some of DS's friends, who moved at 11+ and have spent most of Years 7 and 8 marking time while other children caught up. If your DS has already started French and Latin, they may well have to start again from scratch. One boy told me that he had learnt no new Latin or French during Year 7 and 8 at his new school. In his case, the feeling of being on pause while other boys caught up caused him to be bored and led to problems with behaviour. If the boys move in Year 9, they have all covered the CE curriculum, so are more likely to be of the same level. Even if they aren't, setting is likely to go straight into place as they start the GCSE curriculum.
Pastorally, I think Yr 7 and 8 at a (biggish) prep school are fantastic. Whether they are head boy or Library prefect or cricket captain or head of house, teachers try to find a position of responsibility for every child. It is a great chance for them to try out leadership with support behind them - teachers who have known boys since reception are really keen for Year 8 boys to spread their wings, whereas if they were right at the bottom of a big school, they might feel more squashed.
This of course comes with caveats. If the prep school is small, your 12 year old boy might find that the sport or the music might not be extensive enough. DS had 30 boys in his year group for 7 and 8, but we still found that he needed club rugby and cricket at the weekend. I also looked for a larger local youth orchestra.
Finally, DS was going on to a pre test school, so we were confidentish that he would end up with a place at the end of Yr 8. I can see that if you are not so confident, and you are offered a Year 7 place, it would be very tempting to go for the 'bird in the hand'!
DD, on the other hand, was going to a school where only a handful of girls enter at Year 9. Although we would have loved her to benefit from the responsibilities and privileges at the top of her prep school, we felt that it would be tricky for her arriving 2 years after major friendships had been formed. I'm still not sure this was the right decision, but we will see. Looking at them both this weekend, the 11 year old is certainly finding the transition to 'big school' a lot more demanding than the 13 year old.
Good luck!