I believe the real reason why other alien lifeforms were retconned (except for the subsequent dis-retconning of the Thargoids in FFE) was a pragmatic one.
FE2 came with little icons of the people inhabiting the space stations you docked at. They weren't awesome graphics, even by 1990s standards, but they added "the human touch". And they were, indeed, all human. Creating space stations inhabited by avians, felinoids, walking treoids and such like, would have required the creation of a whole bunch of additional graphics. I guess they simply didn't want to go to that much extra trouble.
Furthermore, sentient life in FE2 wasn't spread out over the entire galaxy like it was in original Elite; it was confined to a small "bubble" of space a few hundred LY across, a tiny speck on an otherwise empty galactic map, much as human life in ED was at game launch. There'd be no reason why all the sentient life in the galaxy would be confined to the same region of space as the one where humans lived. True, they could have made a whole bunch of additional "alien bubbles", but given that it was physically impossible for ships to travel more than 2000 LY in the original ED without their hyperdrives breaking down and exploding, so the additional bubbles would have had to have been closer than this, and without incentives to visit them, they'd have been a whole bunch of extra work (designing alien spaceships, space stations, etc) for not a lot of eyeballs.
Thus, the FE2/FFE lore became that while alien lifeforms were rather common in the galaxy (Earth-like planets were probably about 10 times more common in FE2 than they are in ED), alien intelligent life was rather rare.
They never explained why this would be so, but there is actually a good lore reason once you include the Thargoids in the mix: the Thargoids exterminate any alien civilization they encounter, and have been successfully keeping the galaxy sentience-free for millions of years, thus no alien civilization ever lasts long enough to encounter another alien civilization, other than the Thargoids. It's actually quite a logical (if heartless) attitude for the Thargoids to take: rapid extermination prevents the younger alien civilizations from forming empires of their own and meeting up and forging an alliance against the Thargoid threat.
The Guardians and the Humans were presumably much faster than the average civilization in rising from pre-industrial to interstellar technology. The Thargoids presumably obliterate most aliens they meet before they can escape from their homeworlds.