Everything changed, you lost the good ol 22r/e, went to a 2rz(2wd) 2.4, and a 3rz(4wd) 2.7. The 3.blow went away and came in a great 3.4. The body switched. The ifs switched to a coil and strut from the old torsion bar set up, the steering switched to a rack and pinion. The bodys got better with rust issues, but the frames where prone to failing in tacoma. Their not really that close if you look at them side by side.
The Tacoma also went to a wider track, I know because I had to replace the rear axle assembly on my 93 and the junkyard gave me a Tacoma rear end by mistake...it is about 2 inches wider! Luckily I noticed the difference before I tore the truck apart.