As the owner of both a DI and DII I can say that if the DI had the 4.6 like my DII, I would have never purchsed the DII. Not that there is anything wrong with a DII, the DI just fits me better.
The CDL was in all Discos up thru '99. In the DII, '00 thru '03, do not have it, unless someone has installed one after market. In '04, they were back in. 2005 was the beginning of the LR3. The DII is still capable without the CDL but better with it. My '03 has one.
Land Rovers tend to leak. Why? No one really knows. So keep up with fluid levels. And for your sake, check some levels if you can, before buying! Like the diffs, transfer case and engine (obviously).
Stay on top of maintenance. You should be lurking under the hood and crawling around underneath weekly. That goes for any brand really, but especially a Land Rover.
The roof baskets/ racks are available aftermarket and dealers, depending on what you're looking for. Your choice.
Other than that, they have the same problems any other make has.
