Our wedding is going to be relatively small, skipping the wedding breakfast and about 60 at the evening reception. My fiance is unlikely to have any family at the wedding (no falling out, just logistics), so anybody from his side that does come will sit on a table with us as they won't know anybody else. I'd probably also include bridesmaids on this table, and the best man who doesn't speak much English. Again this is just an evening reception so I don't care if people get up and swap seats, whatever makes them more comfortable.
My parents and siblings will fill a table of their own, and I'm sure my mum would prefer to sit with my older brother anyway so I don't think it will really be an issue for us. I'm thinking of only inviting my dad's sister, even though my mum and dad don't really 'like' her or speak to her, but I'm sure they could get on for an evening, if she even turns up (my sister didn't invite her to her wedding a few years ago which she might still be sore about). My mum doesn't like any of her brothers and sisters and I don't really either so I'm not bothered if they're offended at not being invited.
The way I see it, it's my wedding. I'm not going to go out of my way to do things that I know will upset people, but I don't want to look back and think I wish I'd done that, I wish I'd not listened to so and so... People might think it's weird my parents aren't sat with me, or why didn't my dad walk me down the aisle, but I honestly don't care. It's your wedding.