I have been looking at pictures of both and I see maybe a slight change in body style but I am curious as to what the big differences are.
Yes, the engines are a big difference. The 2nd gen also has head gasket concerns and the gas mileage is usually worse than the third gen.Having owned a '95 2nd gen and three 3rd gens since, I'll never own another 2nd gen. Had a 2nd gen back in college and I'll admit, they look great inside and out, but wow are they under powered. The 3.0L is often referred to as the 3.SLOW, b/c it is just that.
Although they look similar they are completely different. 2nd gen had the 22re 4 cyl (2.4l I believe) or the 3.0l V-6 whereas the 3rd gen has the 3fe (I think?) 2.7l 4 or the 5VZ 3.4 V6.
The drivetrain alone and with an available locker makes a huge diff with a 3rd over a 2nd.
Stock vs stock the 3rd gens are superior in nearly every way if not every way.