I'm not aware of any differences that could be labeled major (frame, suspension, drivetrain, etc.), except for the steel front axle housing, and the slight bump in horsepower (2002, I believe). Early automatics 99-02 (I think...but don't quote me) had aluminum front axle housings. Manuals always have steel. Somewhere in the later models, they went to all steel, but I'm unsure if it was in 2003,04, or 05. It is my understanding that at least the 2005 auto GVs have steel, but you'll want to verify that. Suzuki is known for using a billion different parts on similar models.
I believe the GV got a higher capacity, or at least a much more efficient air conditioning system around 2002-03, although it might have even started by 2001. I would consider this major, living in Florida and owning a 1999. LOL.
I once found info stating that the 2005 received more sound dampening materials (versus even 2003 and 2004), but I cannot vouch for the authenticity of that statement.
I think the 2005 has a different alternator (possibly a little larger) as well. At any rate, I believe that this vehicle was truly perfected by 2005, and would love to buy one in the near future. Every thing is a little better on the 2005s...better rims, great AC, no timing chain problems (though my 99 has 200,000 miles with no problems), possibly quieter, steering wheel audio controls, 165hp, better looking dash (2003-2005). About the only thing I don't like are the silvery, aftermarket-looking, tuner-esque taillights. I much prefer the traditional taillight look.
Oh yeah....one other MAJOR thing (how could I forget?). Many 1999 and 2000s (including mine) had a faulty front 4wd actuator system. Slips way too much when in 4wd on a slippery surface and makes many loud banging thuds...a MAJOR PROBLEM! Chevrolet issued a bulletin on this for early Trackers. Suzuki never did a think. Do yourself a favor, and try to get an 05 if you can. Otherwise 2003-04 are nice, too. Hope this helps a little. I used to remember the dates when things changed on these trucks, but I've been out of the loop for a while and have forgotten. Good luck.