Spoilers were a FACTORY option on in 2000. They were a DEALER installed option before that.
As for the difference in wheels, when I first saw the photos of the E1 with the new style wheels I felt somewhat cheated. Once I parked my car next to one with the newer style wheels I felt that the new wheel did not look nearly as good in person. For a while I felt that the new wheel was perhaps slightly better looking, but not enough to buy another set. As time has passed, I kind of feel that the car looks better with the old style wheels.
What it boils down to, in my opinion, is that they both look good. It's a toss up.
As to which year is best is also a toss up. Along with the upgrades (better front strut valving in 98.5 and 5 moe HP in 99) there was also decontenting that went along with it. Thinner sun visors, no trim around the trunk release lever, removal of the counterbalance from the glove box door, less content on the gauge faces, slightly less displacement, revised exhaust pipe routing, and the list goes on and on. The most insulting of all was the deconting of the quality of the dash glue on the 99 and 00.
