Villa or hotel depends on what you do / don't mind doing IMO PrincessIrene . I think villas are maybe cheaper (?) if you'd need more than one hotel room and more room to move around if you have a few kids. I've done it both ways and wouldn't do villa again. We made the switch to staying in Disney hotels and would never do anything else now as we enjoy the perks. But I am not one for self-catering trips anyway as I want a break from housework / cooking when on holidays. You can eat out of course but I just like having my bed made for me every day 
Hotels are my treat thing, so that's just a personal preference. Disney hotels have lots of perks to make up for the extra expense (they are more expensive though there are deals) and most of them are really well themed. If you don't want to hire a car there is the transport network etc and extra magic hours / having your shopping shipped back to your resort, all sorts of things. I find it good value even though it may cost a bit more; it can be quite an intense holiday activity-wise and some of the perks just make it a bit easier. Also if you book at the right time (and stay at Disney) you can get free Disney Dining Plan, which we have had for the first time this booking and it's going to save us A LOT of money on food.
We added tickets for Universal but are kind of regretting it now - DH and I really want to see the Harry Potter stuff as we missed it last time (pre-kids), but I don't think our 4 year old son is going to get anything out of it. He's not into HP yet and most of the rides will be too big for him (even stuff like the Minions ride). The rides there are more full on so tend to have bigger height requirements than Disney. A 9 year old might love it though, depending on how into intense rides they are. There is superhero stuff there but it will be disappearing as the Marvel licenses move over to Disney. There will be superhero stuff built at Disney parks, but it will take a number of years, same with expanding the Star Wars parts.
We are stuck with the tickets now but for our next trip (when DS is 5) we are probably going to skip Universal and either do Legoland or spend extra days at the water parks. Maybe we can shoehorn him into HP before then and he will be interested but I am anticipating DH and I carting a bored kid around Diagon Alley in a buggy and having to do the big rides as Single Riders!
There's a ton of options, but they are all pretty great and 3 kids are going to love it regardless! We have been a lot and have never done the level of planning that I'm doing this time and it's always been wonderful. So many people will have their own 'best' ways of doing it that they love, really the considerations are personal ones : budget, amount of space, convenience, how much you want to get done.