Well, you have to decide what your priorities are. Do you want something newer? Do you need more room? Do you need more power? Do you want simplicity or do you want stuff like Airbags, ABS, etc...
Other thing to keep in mind. Defenders are going to be more rustic. Even with a hardtop, the windows do not roll down, they slide. (Except for the '97 LE) Parts are going to be harder to find and if you go to the Dealer, more expensive.
Yes, the Rubicon has lower gears but it doesn't have a V8 backing it. Swapping axles on a D90 are easier then on the Rubicon. The D90 had third members which means bench gear swaps. The downside is that the axles use closed knuckle design. Still the Rubicon's have their own problems. The front stub axles were prone to breaking for some reason and the rear D44 still uses D35 outer axle tubes.
Really, though, the D90 will attract more attention since they are rarer. A clean one is hard to find since most people seem to have held onto them. Most will have close to 100K miles on them because of age. The Rover V8 is a good engine. British Leland's best, actually.
As for best, that's very subjective. 'Best at what?', should be asked. I think both would be more then you'd want/need.
Keep in mind the Defender series continues on in the UK and is currently used by SAS, ADF, as well as some USSOC. Don't confuse the Defender with the other Rovers.
