Depends on how much you want to modify it. The more aftermarket stuff you swap on, the more you negate any benefit of the different years. Fuel injection is nice, but very rare (read hard to find / expensive). I've owned 3 carbed sami's and they run just fine.
And honestly - look into getting a 2 door tracker / sidekick. They're a MUCH better value than the samurais these days. Better power, better fuel economy, much more room (while still retaining the small footpring / lightweight), better suspension (coil), and better interior bits (cup holders, radio, seats etc) - and, they're CHEAPER! You can lift one 2" for around $300, and slap 29/30" tires under it and be good to go for all but the most extreme / insane of obstacles.