The villas come with a chef and host so you can have your meals in-house (and cooked more to order), plus there's the obvious much larger spaces, entertaining, living and dining areas etc vs the pavilions.
It's really almost a whole different/new product within the resort itself - sort of a mini resort-within-a-resort type thing. The villas are HUGE FYI. It really is a totally different experience.

Of course, beyond that, you'd all be under 'one roof' (not literally in this case because of how the villas are laid out but basically you'd be in your own mini 3-bedroom resort) vs three separate pavilions, even if nearby - of course while still having access to the rest of the resort.

Each villa is quite different too, so check in with the team to see what's best suited for you - there's also the question of old villas vs new ones (I much prefer the older ones, even if some of them don't have ocean views - they're built around a centrally structured pool for the most part - whereas some of the newer ones have nice infinity pools, but they feel more of an after thought. The newer ones also face the back side towards Thalang - still nice views, but not as nice as the older units in terms of views IMO) - but your mileage may vary.

Depending on how old the kids are, you could possibly get away with a 2-bedroom pavilion if that is still your preference.