In 99 the base model had a 5 speed automatic (lower gearing)
(and I believe the 99 T5 still used the 4 speed automatic).
This is from memory.

The base engine also had variable valve timing. Actually, I think
the T5 does in 99 but one of them had it on exhaust and other on
the intake (I forget which had what).

The T5s/GLT have same suspension which is a bit stiffer then the
base model. I'm basing this on a base model rental I once had
for a weekend (very soft compared to my 98 T5).

T5s typically came with leather, sunroof, heated seats, fancy
sound system, etc. Basically, they were loaded.

The big changes in 99 applied to all models and included one
coil per spark blug, electronic "drive-by-wire" throttle, updated
front/rear brake force distribution circuit (some complain it
felt like ABS kicking in), introduction of 5 speed autos, introduction
of variable valve timing, all engines got oil spray on piston bottom
for improved cooling (previously only on turbo engines). Quite a
few improvements on the 99s vs earlier cars. Again, all from memory
so don't quote me on it :)