We stayed at the Novotel Nusa Dua last year with our two kids. We had a 2 bed apartment. The pool and bar area was lovely and there are restaurants nearby (a free shuttle bus takes you there and back every 30mins or so?).

It's a bit of a drive to Kuta but we weren't really interested in going there anyway, only went once! Depends what you want really! I preferred Nusa Dua at the time as I'd never been to Bali and it felt safer (gated security at entrance plus each hotel has its own security). But I'm a worry wart lol! Seminyak is supposed to be really beautiful and I'd like to visit there if we ever go back!