'03 will be the last of the line Thundercat-powered (carb-fed) FZS6 Fazers (killed off by emissions rules), replaced in '04 by the R6-powered (albeit detuned) (fuel-injected) FZ6 Fazers.
The general consensus is that the older Fazers were nicer to ride (carb-fed, so no snatchy fuelling at low speeds), although some will no doubt disagree.
The 2007 (S2 models) brought a few changes: new swingarm, bolt-on pillion pegs (rather than the previous welded-on ones), slightly different front mudguard, differences in the fairing, different clocks, 4-pot monobloc brakes from the R6 (rather than the 2-pot sliding pin calipers), and a different fuel map.