I currently have both and I'll tell you, the ride is soooo much more comfortable on the DI. My experience with my Disco is that it has been a money pit. And now that it's finally running well, has all the accessories I wanted, I get the itch for a D90.
Echoing what's already been said, but here it goes. The D90 is so much noisier, bumpier and quirky (it's manual). The DI has more space, both leak water like a sieve and I know to expect most of the same mechanical problems on the D90 that I've had on the DI.
But make no mistake, a modded DI has a cool factor all it's own. Both vehicles attract attention and rubbernecking when on the freeway.
D90 folks are going to flame me for this, but given the choice, I'd keep both and continue to use the Disco for offroading. The reason is that a) I fear f-ing up the body work on the D90 b) I fear affecting the resale value of the D90. The Disco has devaluated such that short of a blown engine, it almost can't go much lower.
In summary, for those who won't or can't have both, the winner will be determined by each individual. Some people prefer a cold, leaky, uber-cool, relatively expensive D90 over a more comfy, refined ride, spacious yet capable Disco.
Javier