1. I generally like to hit up Universal first and finish with Disney although on this last trip, we mixed it up by visiting Universal in the middle. It made for a nice change. Either way works but what I'd suggest is looking at the park hours for both places and also when EMH are (Assuming you stay on Disney property). I visited IOA on a Friday (when it closed at 7), and then was still able to enjoy Epcot that night because it had EMH for example. I'm not an uber planner but I do decide which parks I'm going to visit which days based around park hours. Also, avoid MK on Saturdays if you can help it. That was the day I choose to go to Uni on my last trip, and it was very relaxing.
2. I think 2 days at Universal is plenty *right now* (I think I might give it 3 days in the future as more things are built). And the rest of your trip can go to Disney. But I do really encourage that you give two full days to Universal. I'm not sure of their summer hours, but at least in February they closed earlier than the Disney parks so if you really feel like it, you might get in a few Disney park hours at night.
3. I absolutely adore the Universal hotels. They are honestly great. So if you feel like you want to swing it, I say give those two nights your doing Uni to the Universal hotels. As others have mentioned, you get the express pass that way. It is a great bargain getting to bypass all the lines with one pass. That being said, if 2 hotels is too expensive or too inconvenient, which is understandable, staying at Disney and having Mears/a cab/your own car bring you over, that is fine too. I've done both options with no problems.
4. Can't be onsite truthfully. The bus and monorail system make things really easy for getting around. Just can't beat it not having to worry about driving too much. Also, just a tip, look at priceline or similar sites for deals for the hotels. You do NOT have to book directly through the Disney site to end up at a Disney hotel with all the perks. You have to book out far enough, but for instance, I was messing around with priceline today, and they had deals for 24 of the Disney hotels plus discount deals on tickets and flights. I compared it with going directly through Disney and not shockingly Disney is more expensive. So again, please don't think you have to go directly through the Disney site to stay at Disney hotels
5. I really enjoy the water parks. I wouldn't say they are worth a full day but at least a half day. @
ParentsOf4 wrote a great treatise on what to do at BB if you do want to stay a full day though. I generally go to each of the water parks in the morning and stay til early afternoon. That way I can go back to the hotel, get cleaned up, and still hit a park. If I were you, my trip would look sort of like this: First two days at Uni, then Disney for six days. 4 days allows for spending a full day in one of the parks. Plus, you have two days to revisit parks, go to DTD if you so choose, do the water parks or even play a round of mini golf (which I also recommend).
Bonus: Random tips for WWHOPP. If you stay on site, you actually are allowed in an hour before the parks open, which is great. If you don't, get to the parks by 8-8:30 so you can get in line to be let in. Go directly to the back of the park to HP. Ride FJ once while taking the regular queue so you can look at literally one of the greatest queues ever made. If you want to reride FJ any other time, take the single rider line. Seriously. Take it. Yes, your party may get split up but this is honestly not a ride where you are paying much attention to anyone else in your party. And waiting 5 minutes to get on is a whole heck of a lot better than waiting 55. This honestly goes for any of the attractions with single rider lines in the parks, but especially for FJ. If you didn't feel you got to see enough of the queue, there is a walk through you can take. After you ride FJ once, go to Ollivander's before the line gets too ridiculously long. I didn't find either of the roller coasters had that bad of waits, but I'd still recommend doing both of them, even Flight of the Hippogriff because it has a cool queue and riding past the hippogriff is so much fun. Dragon Challenge doesn't have that great a queue but it is a fun ride. Try at least butterbeer though I'd also recommend the pumpkin juice. The Cornish pasties at The Three Broomsticks are good. Go in the shops... there is so much fun stuff to look at even if you don't buy anything, and also make sure to look at the window panes!
