The two editions are swings and roundabouts, really. I like some of the stuff 2e does better than 1e, but I also like some of the things 1e does better than 2e. Broadly speaking, characters are less competent in 1e - that is, they're less likely to succeed at basic tasks - and the feel is much more one of a hostile universe waiting to kill the unwary. 2e is a bit more heroic (though the universe will still totally eat you if you're stupid), and the characters are somewhat more combat capable and better rounded. Plus I really, really like the freedom of the aptitude system in 2e instead of the advance tables that 1e had for the freedom they give in making your character what you want it to be - but it does make spending experience a bit of a nuisance sometimes, especially if you're new to the system.
I don't think 1e and 2e will be going out of print any time soon - not as long as Ulisses has the rights to them and are making money off them.
I don't know much about the new 40k line, though, I'm afraid, so can't help you save to say it's a very different mechanical base. They've dropped the percentile system, in favour of... I think a d6 dice pool system? I forget. I sort of decided I wasn't that interested at that point since I really like the d100 system, though I'll probably check it out when it comes out just in case I really do like it.