Most likely reason is that iOS4 was already in development by a different team... The iPad was something that was done by a very small team in complete secrecy away from the rest of the iPhone and iOS groups. As a result, they used the iOS3.1 as the starting point for the iPad to make 3.2. (They had to, 4.0 wasn't even close to being finished...)
All those things they added into 3.2 need to be ported over to 4.0, as well as all the app changes (calendar, mail, etc.). It wasn't done before this because until the iPad was released into the wild with 3.2 finalized, those resources (those that worked on 3.2) weren't freed up to work on the porting to 4.0 effort. So it's going to take a little bit of time to get them moved over to 4.0. I'm betting we'll see something by Sept or Oct at the latest, and every version afterwards should be simultaneous.
Some people just don't get how much time and effort it takes to do this sort of thing, especially at the OS and app level. The hardware might be very similar (99% so) but there ARE differences (screen res for one) that need to be taken into account and dealt with. Think about it, EVERY app was changed at least somewhat on the iPad vs iPhone 3.1...