Why the hatred for Mega Man X6? X2, X3, and X5 were all worse IMO. X1 was the best, though, and should have been a stand-alone game with no sequels.
Anyway:
SFA1: good Lord, what the heck was Capcom thinking releasing this crap? It looked like it predated both their Marvel and Darkstalker games by a good 2-3 years. Shared backgrounds (and bland ones, Chun-Li and Charlie's stages notwithstanding), bad balance, crappy characters like Birdie and out-of-place new ones like Rose really caused the game to fall short of what it should have been. SFA1 should have been what SFA2 was, and I can't help wonder how much the series would have benefitted if it was like Alpha 2 right from the start. At least it had Charlie, though.
Soul Calibur 2: Man, I don't even know where to start with this one. They ditched my favorite characters (Hwang, Seigfried, and to a lesser extent Rock; and yes, I know about the Berzerker guy) and didn't even bother putting another (Sophitia) in until she became a console character. The gameplay is identical to SC1, the storyline is essentially the same, the final boss is the same, the graphics took a hit (only Rafael's mansion is worth noting in terms of backgrounds, and to see what I mean character-wise, look at how tiny Sophitia's eyes are compared to everyone else's, especially Talim; also look at how shrimpy Cervantes looks compared to his previous incarnations), the new characters sucked (except for Rafael, whom I think is the best new character in the series thus far), the girls had a goofy-ass DoA physics problem going on which really didn't fit with the serious nature of the series, the narrator was barely involved (a touch I really admired before), the endings were lazy as all hell (an incredible ONE new piece of artwork for your character?! That's the best they could do?! At least in SC1 there were 2-3. The first picture for character endings in SC2 is just the standard character art seen in manuals, marquees, etc.), the mission battle was a snooze (labyrinths -- 'nuff said), shared backgrounds (was this a first for a 3D fighter? Either way it's inexcusable for a game that came out four years after the previous entry), and the most laughably retarted, poorly designed, and most misplaced character ever in a fighting game (NECRID). Even the intro was a let-down. SB/SE and SC1 was just instant immersion that started slowly but really got going towards the end, while the music and directing in this one fell flat right out the gates and never really built into anything, save for Mitsurugi's neat ambush. The extras paled in comparison to SC1 (the art gallery was phenomenal in SC1 and the fan art was a great touch) and the Weapon Demonstrations were copied and pasted. Seriously, what did Namco do during those four years between the two? This should have come out a year later, tops.
Um, that was longer than I thought it would be. Guess I'll stop there.

But this game just totally killed my feelings for the series as a whole. SC1>>>>>>>>>>>>>>>>>>>>>>SC2. SE/SB may have less depth gameplay-wise, but the variety of music available (3 soundtracks to choose from is too awesome), "theatre"-like atmosphere, and the fact that the characters don't look like a random bunch of fighting game characters drawn from a hat puts it well above.