I'm bored, so I might as well chime in my opinion on this dead horse.
I do not own any SFB materials (other than the Cadet version or whatever it's called that came with SFC), have never even looked at them in fact. I'm not overly into Tabletop Wargaming either, I'm simply an average gamer (well... not quite perhaps, I prefer RTS's over FPS, only own a single FPS which isn't quite average of your typical gamer nowadays).
I do have all of the SFC titles (including SFC1 Gold) and of them, I must say I vastly prefer 1, 2, and OP to 3.
There's just so much more to do, more races, more weapons, more systems, more singleplayer campaigns (very important to me as I don't really play on-line very much), more ships, just more.
3 just didn't have as much to do. While you could argue that 3 has more ships because of the ability to refit your current ship to something else, it just didn't seem the same, I can change my phaser types all day long and the ship just doesn't seem any different, and I really miss my T-bombs.
AV could have been handled better in my opinion, or perhaps cut out all together. Combat also was disappointing, the fact that if your ship gets caught by a ship with more room for a larger tractor there's didly all you can do to get out is annoying.
As far as the campaign went, it was not bad but too short and too rushed. I really disliked getting moved around the map with no time in-between. The campaigns from the older games were just as interesting and lasted longer as well.
There are certainly things I like about 3, they've mostly been mentioned already by others, the things like bringing the Officers back from SFC1, some of the D3 features, reverse is handy, not sure about warp can't decide if it's benefits outweigh its disadvantages, hidden cloak.
So to sum up, I've never played SFB, am not in the least interested in ever playing SFB, and wish SFC3 was based off SFB rather than what it is just from playing the previous games that were based on SFB.
Of course this is all my humble opinion and I'm sure others will disagree, I can understand, and to be honest, being able to play the previous titles is good enough for me, I have what I want (well... as close to what I'm ever going to get most likely at least) so I won't begrudge those who got what they wanted in SFC3.