Homeworld's awkward interface and camera control was one of the reasons I never got into that game.
But it wasn't a sufficient enough reason to damn the game to a poorer mark that it got. I very much doubt Homeworld would have been considered so revolutionary if it didn't have the total freedom of movement.
I'm not saying the 3d movement made Homeworld revolutionary all on its own, but it was certainly a major factor. Even if this weren't so, I totally disagree with you

I found the camera intuitive and and easy to use, same with the interface... but that's just me

The freedom to move like that is what is important, rather than the need to.
There is no 'high ground' in space, so there is no tactical advantage the 3rd dimension unless you start talking about hitting a specific weak part of a ship or something...which a game of this scale does not involve. Hence, for the combat, 3D adds nothing.
True enough, but, as someone who hasn't played the game, could I ask: Doesn't 3d double the flanking opportunities? Furthermore, if everyone thought the 3d environment were useless, couldn't you surprise them? Isn't that part of the game? In my opinion, it's better to have that ability there, without forcing the players to use it - that way, everyone's happy

and it doesn't detract from the game.
Besides, how would you feel if you were up against a turtle who forgot about the other dimension, such that he only defended laterally? In a totally 2d plane, you (or at least I) would be hating the developers for taking away that part of space combat that would win me the battle.
As far as planets and stars all being along the same plane, it is true that a true 3 dimensional map would add something to gameplay and tactics, since there could then be more links between planets. However, that said, this small benefit is far outweighed by the huge issue of playability.
I actually agree with you that planets and stars should be in a relatively 2d configuration, but for a different reason.
The plane of the ecliptic.
'nuff said