Doing everything separately is a lot cheaper than booking, say, a Disney hotel through a package deal, though I've been looking lately and it is a lot more expensive than it was the last time we went about 5 years ago, even more so if you're having to go in school holidays (we don't have children, so it's much easier for us I know).
I would NEVER go in the summer holidays though. Far, far too hot. End of May was too hot for me!
We book everything separately - flights directly with whichever airline gets us there cheapest and with reasonable flight times, villa through homeaway, car hire through Alamo using a "Brit" discount (seriously get the Brit Guide to Orlando book - brilliant advice and the Alamo discount code saves a fortune), park tickets in advance through Attraction Tickets Direct in the UK.
It's by no means a cheap or relaxing holiday, but we love it. We tend to go to a park every other day, and make sure we do a fair amount of non-Disney/Universal stuff too. A lot of people go to the parks early, back to the villa in the heat of the day and chill out by the pool, then back to the parks in the evening for their shows/fireworks.
Are your kids in to this sort of thing? I have some friends whose kids were brought up on Disney films and they absolutely adored it, but I have others whose kids were very nonplussed about it all, and it was just like any other theme park to them. They've really got to buy in to the whole Disney thing for it to be as magical as it can be, especially for the money you pay. I'm not a huge Disney freak, but there's something about Magic Kingdom that just makes me well up every time I go. (I know... I'm sad)
I would say though if you feel it's going to leave you tight on a financial buffer, then seriously consider whether it's worth it. Yes, you can't put a price on memories, but if those memories include you spending the whole holiday worrying about how much you've spent, then you're not going to enjoy it either.