I have done a similar itinerary to you, but during February instead and picking North Island in the Seychelles. The difficulty is the weather, which Pausanias has kindly already described - as one will be in peak whilst the other is not. We had this issue and just bit the bullet on it. When we stayed in Cape Town in September last year, it was mostly wet with very occasional sun; we went back in February and it was perfect, but then the Seychelles is still off-peak (but we got lucky and had no rain). Seychelles could be the most expensive part of the trip, so worth taking the least risk on and therefore it's not the end of the world with Cape Town's potentially inadequate weather, but worth thinking about.

If you're going to Franschhoek then without good weather it's a bit pointless, so you'll want to be aiming for September, then only Cape Town is the risky element of the trip. We stayed at La Residence and went for lunch at Leeu Estates one day - personally I don't think they're really competition. La Residence is a unique, beautiful property, whereas Leeu Estates feels soulless. It's an impressive property, but it felt like it could have been anywhere and did not wow me. I wouldn't be upset to stay there, but I was glad we picked La Residence over it. Food was good though - as it seems to be everywhere in South Africa.