Just in case anyone is interested - in the end we spent a week at Fregate and then a week at Maia.
I managed to fall over jogging in the jungle on Fregate on day 3 and ended up limping out of the jungle bleeding copiously and had to get taken to the nurse. It's still a little painful to walk two weeks later.
Despite this we had a fantastic time at Fregate - it's really special and we actually felt like we could have stayed for a lot longer than a week. There is a ton to do, lots of awesome beaches, some cool hikes, and the fact that you feel like you've got the Island to yourself makes it really fun. I think the only thing we thought they could have done better was the food - they were good at customising if we asked to stuff but there wasn't anything particularly interesting / innovative on the menu and sometimes simple stuff was poorly executed - for example my eggs benedict was nowhere near having runny yolks. But that I think is the trade-off - we had dinner in 7 different locations on the 7 nights and so they transport a chef to you to cook for you - which I guess means they lose any of the benefits of specialisation.
The hard product was also fantastic - two massive pavilions with an adjoining 'room' in the middle and an infinity pool actually long enough to be a lap pool (well, I would estimate 12m long or so). The gym was ok (running machine, cross trainer, and a non-functioning bike) and the spa seemed nice but I'm not really an expert.
Maia suffered by being second on the itinerary. The food there was definitely better and they were excellent at customizing. We're not normally tricky customers but a slightly patronising waiter told us to 'challenge' him so I asked for Pani Puri (my aunts make some mean Pani Puri) which they did with aplomb. My wife has a nut allergy which they dealt with well too.
The hard product at Maia is very good but suffers in comparison with Fregate - it looks a bit more tired and the pools are shorter (think maybe 7-8 m.) The bathrooms with the outside baths are very neat and I think if we'd gone their first we'd have thought it was awesome. As it is we spent most of our time by the (very empty) poolside area.
Both Maia and Fregate came with some included booze - Fregate had 3 different whites and reds and Maia came with c.12 of each and a long cocktail list that was also included. Neither wine list really grabbed me (as in, I don't think I tried any wines for a second time...) but my tastes may be a tad particular- Maia's definitely looked like a good try. Both had non-complimentary wine lists included too which seemed fairly comprehensive.
I think my biggest gripe with Maia would probably be that I'm not really sure what its raison d'etre is- what is the point of going there to stay? We had a perfectly nice time but really could have been anywhere in the world. I would guess its the food and drink - they claim their food is the best in the Seychelles - and maybe we weren't blown away by that because we normally eat out in London which is a pretty decent benchmark. And I may be being a bit unfair to Maia as it did have to follow up an amazing stay at Fregate.
I did a dive discovery course courtesy of Maia which happened to drop some people off at the beach at the FS. My (totally uninformed) view was the FS looked massive but it did also look like it had an excellent beach.
Other holidaymakers were very very complimentary about La Digue, and fairly complimentary about Praslin. Desroches also has a very decent rep. If we ever make it back I think we'd definitely go back to Fregate and then try one of L'Orangerie / North Island / whatever ends up being built at Desroches.
I'm sure MacMyDay will end up writing a much better trip report in a few months time so I'm going to stop there but feel free to PM me if you have further questions.