I loved them both, but found HW2 nicer to play due to the UI improvements. I've heard that storywise it was a disaster, with people refering to the "Dustwars" design document.
Homeworld was a thing of beauty, ship designs, story and campaign, music, the first to have 3d movement (AFAIK). It was just great. Unfortunately, i got it so late that graphics-wise it was outdated, but i'm not graphics-(you-konow-what), even though i own Crysis 
Sins is very good too, but not "homeworld" great. Sins has a backstory for each race, but it does nothing with them, since there is no campaign to drive the stories forward. It's up to you to "roleplay" the races.
BTW, now that relic has the Homeworld license back, there is a chance we might see Homeworld 3, there are even a few hints suggesting it could already be in deveploment: http://www.eurogamer.net/article.php?article_id=318681 