Hi there - I know this a few months old but your kids aren't starting until Sept 2014. I have experience of a few of these schools... (Also just moved to Exeter ourselves 18 months ago from London - I grew up here).
I went to Colyton Grammer then St Margaret's (less a ademic than Maynard, closed last year). At the time, Exeter was all boys apart from the 6th form and the St Margaret's / Exeter 6th forms were almost joint, with many subjects taught jointly (all my subjects were taught at Exeter in mixed groups). One of my brothers went to Exeter, the other to Blundells. I now have a school age daughter at Cathedral School. So....
Colyton Grammer - very "grammerish". I loathed it, as did my parents who took me out for year 10. I think at the time it was partly snobbery. They'd both been to v famous boarding schools and found Colyton basically too state! The education was, for me, not at all rounded and v pushy. I loved music and drama and wasn't really encouraged in that.
St Margaret's - irrelevant because its closed, but it was all girls (like Maynard) and I HATED that aspect.
Exeter School - I loved the subjects I did there and my brother also loved it. It is good pastorally (my bro was there relatively recently, under the current head, and a family crisis was dealt with v well) but I would say you need to be relatively robust and academic to really thrive.
Blundells - loved by my brother but v long days (he was flexi boarding, school bus from Exeter). I know he got v exhausted to begin with. But.... It's the school I plan for our kids once older. You need to be aware that it certainly was (my brother left 7 years ago) a boarding school and day pupils really don't get as much out as boarders. I would say you need to plan for at least flexi boarding from 11, or 13.
Cathedral School (not on your list I know!) - we love this! DD is thriving there. The beauty of it (for us) is we can choose secondary school at 13, when we've actually figured out what would suit her best. In the meantime, she can enjoy a not too pushy, very family orientated school that we can walk to. We find it excellent!!
Re areas, Topsham is indeed lovely but rather "twee". I would choose Lympstone instead, and you then have the option of the fab St Peters prep school. St Leonard's is nice. As for villages.... I don't know many well, but all the villages in the valley road from Exeter to Tiverton are lovely and are popular (Thorverton, Silverton and Bickleigh in particular). Chudleigh is very popular but is on the other side of Exeter, so no good for Blundells.