This question is actually contentious. Many fans prefer the 94 version as it retains the iMuse adaptive music system which brings a lot of flavor to the game. The graphics are indeed improved in the 98 version, but it no longer has adaptive music and all the music is different than the music that came with the original game. Also, I've heard there are some issues with the new engine messing up the timings in some missions.
Having said that, the 94 version suffers from some timing issues when running on modern processors through DOSBox that can be hard to fix. There are a bunch of other threads about that around here, it involves messing with the cycles settings in DOSBox, and I'm not sure there's been a consensus on the best settings yet. But people are still working on it.
The case of TIE Fighter is even trickier because the Collector's CD from 1995 allowed for 640x480 graphics (instead of the 320x200 you get with the early versions of X-Wing) so the graphical improvements in the 98 version aren't as pronounced. And the 98 version has the same music problems plus a bunch of other little details. That's why I and many others perfer the 1995 verison for TIE Fighter, although again there are timing issues when running it today that can be annoying to deal with. Some people in these forums are actively trying to find the best workarounds though.