In many a gamer's mind, the Megaman X series started and ended with the first X game on SNES. Of course, being Capcom, eight Megaman X games were made, including 2 sequels on the SNES. X2 made a number of improvements to the original Megaman X, including the X-Hunter sub-boss series, the ability to store two charged shots, and, most notably, airdashing. The only real step backwards in X2 was on the sub-weapons, which were much more generic and not as useful as those in the original Megaman X.
X3 continues on the steady refinement of the Megaman X formula begun in X2. The X-hunter concept is refined a bit with Bit, Byte and the return of series favorite Vile. It's pretty cool how the way the player deals with these characters early in the game affects the endgame. Whether and how you kill off these three characters changes what bosses you face later in the game, and even is tied to a crucial "secret" weapon!
Also, Megaman X's upgrades have been tweaked in X3 to give players new options. The helmet upgrade is finally put to a decent use, allowing players to see a map of an entire stage and highlighting where hidden items may be found. The arm upgrade, in addition to looking cooler in this game than previous games, allows for combining charged buster shots into a wall of destructive power. Megaman X can also air dash straight up in this game, making some of those difficult platforming sections a bit more interesting. Level 2 enhancements have also been implemented, permitting Megaman X even more wild abilities (double air dashing, anyone?). Lastly, ride armors, sort of a gimmick in previous games, have been expanded upon into a core game mechanic. Giving players 4 different flavors of ride armor, accessible in every level, is insanely fun, even though the system is somewhat buried into the game, and could have been made more visible. If you take the suggested sub-boss path, you only get the ride armors in the last stage. After seeing how cool they were, I felt a bit cheated not having access to them earlier.
Level design seems a bit improved in X3 compared to previous versions as well. Megaman X and X2 always had a secret or two that was totally unintuitive, or a platform sequence that was insanely difficult for no reason. X3 has none of these frustrations. There is always a hint to the player as to where to find secret upgrades (well, except maybe for the last, best upgrade of them all), and I never encountered a platforming sequence that required me to hit an obscure edge, like the first two games.
It was nice to see sub-weapons be more unique and useful in X3 than compared to X2. I found non-boss uses for about half of the sub-weapons, which is above average for a Megaman game (and far more than X2, which I almost exclusively stuck with the default buster).
Finally, X3 is the first game that lets players play as Zero. While the experience is generally limited to non-bosses, it was very cool to be able to finally swing that Z-saber around and wipe the floor with some mavericks.
However, as in X2, there are some irksome steps backward in X3 that keep the perfect Megaman game elusive. Most notably, the difficulty in X3 is heavily skewed towards the beginning of the game. All the sub-bosses (particularly Blizzard Buffalo and Tunnel Rhino) were extremely tough to fight in the early game, when you have a short life bar and few sub-tanks to take them on with. It took me longer to get through the first 3 stages of X3 than it did to get through the rest of the game!
On the flip side, once you get powered up, X3 becomes a bit of a cakewalk until the final boss. This is a stark contrast to the first two games, which had a more progressive difficulty system. This is a step backwards in design in my opinion, as I could easily see more casual fans throwing their controller down for good after dying many, many times early in the game. Other nitpicks I would have relate to the helmet upgrade (why don't players have access to the level map after the beginning of the level) and the arm upgrade (the upgraded, lvl. 3 charged buster is slower and has a wider hitbox, making it less precise than the default lvl. 2 charged buster). The most annoying thing about Megaman X3 is that it's very clear how X3 could have been an almost perfect Megaman game, had they just spent a little more time ironing out these kinks.
Still, in all it's hard not to say that Megaman X3 is the best of the SNES Megaman X trilogy. It's a bigger, more challenging game than either of its predecessors, and above all, is a ton of fun. Just don't make it your first Megaman X game, because it will kick your ass repeatedly until you develop the skills to pay the bills.