I myself prefer 4th, (as does my one friend who lives and dies by Shadowrun). I am an oddity here in my gaming community of those that like to play the game. Most people I know who've played prefer 3rd, or a hybrid of 2nd and 3rd.
4th was a straight forward, elegant mechanic, that makes the game very playable. Most of the people I know who dislike 4th feel that the characters are too weak as compared to other editions. They've diminished the power in other words. I'm sure other's on here can give you a much better overview than I (Woodgolem comes to mind as he is my friend who loves Shadowrun, cut his teeth on Shadowrun, and prefers 4th to other editions).
SR4 is a good system. If you've never played SR before, I'd actually recommend it over other editions, easier to learn though the character creation of SR4 sucks IMO. The mechanics are pretty decent, the updated wireless world, while cool, give me headaches just trying to comprehend all the ramifications.
That said, I prefer SR3 (or SR2). Not because they are "better", I just was brought up on SR with SR2 and SR3 is similar enough that it is still intuitive for me. I like the damage codes and how armor works, etc. To me, an Ares Predator is supposed to do 9M damage, not 5P (in SR4).
The world of Shadowrun is pure awesome and I love the RP possibilities. You can have essions doing runs, building more contacts, looking for some sweet gear, hanging out at a bar, chasing down the local poli-thugs, etc. I usually leave my SR games wide open and see where the players want to go with it, and its an easy setting in which to do that.
If you do go SR3, you can still find most of the SR3 books still new at various shops. I order alot from NKG, they have a great selection of SR products.
Third edition is where I started playing the game, and frankly it's sort of where I began my love of Role playing games in general. But for all the love I have for the game there are some seriously confusing aspects of the game. Vehicle Combat was commonly banned in my gaming group and the number of people willing or wanting to play deckers (renamed Hackers in 4th) was few. I mean who wants to be completely useless for an entire adventure accept for the one moment were everybody else is bored. With making the Matrix wireless it means that you need to have the hacker running around with you and adds a surreal component to the game with the Augmented Reality mechanic and idea.
From what I've seen most of the people are complaining about the lower power nature of the new mechanics. Which from my point of view makes sense. The game is supposed to be about people living outside of the law and doing battle against monolithic and indestructible corporations who use them as pawns in big games of looking for profit at any cost. (That was a long sentence) But anyway it stands to reason that you wouldn't have the ungodly power that many of the previous additions would give you access too. The new version is a much more subtle and smooth game then it's ancestors. It's a lot more about getting out by the skin of your teeth and wits then about powering through the bad guys. Think heist movie versus thriller.
But anyway I like 4th cause the lower powered feel is truer to spirit of the world in the game though perhaps a deviation from it's ancestors.
ShadowRun 4e is the current one, and the system is very cool in my opinion. It's a bit of a change from the previous two editions, but not so drastic that those playing the older editions cannot adjust. Spellcasting and magic are nicely done and "decking" is much simpler and less of a distraction to the game than prior editions. I haven't looked too closely at rigging, or exploited the wireless world much so far, but I do recommend 4e.
I really enjoyed all the prior editions, of which perhaps 3e made the biggest jumps in making decking faster. Of course, I completely enjoyed the gritty 1st edition, which was at times rediculously overpowered. Nothing like flinging 30+ dice for one attack.
I think in 4e there is more attention to balance between character types, though it still seems like a mage/shaman/adept is pretty much required. Through a few scenarios, it seems like resource management is key. In combat at low levels, players seem to have the option of being very defensive and taking minimal damage and inflicting minimal damage, or going all out to land heavy blows but leave themselves open for counterattacks (if the opponent is still standing).
Still, if you have players who like 3e, and it's a bargain... 3e is super-fun on its own.
My understanding is that there is pretty big edition split between 3e and 4e. Check the I {heart} Shadowrun thread, I think it goes into detail on the differences between the editions.
Shadowrun isn't d20 is it? While I don't want to critique other gaming systems, I'm not really motivated to spend time learning a completely different rules system.
For me I have played 4e a bit and tons of 3e (even got some playtesting credits to the fact.) For me I still prefer 3e but I think that might have to do with the fact that I do not appreciate the huge change that happened between editions. I have every Shadowrun book produced since 2e and the 3e books are immaculate even after FASA closed. But the fact that the transition to Catalyst basically tanked everything.
I think if Catalyst really wanted to win people over would be to go back and work out a system to change characters over to the new system as not only are the adventures good but a lot of us have characters that we really want to carry over...lol
As for game mechanics I like 4e, the system is very straightforward with some nifty little tricks. Like I love when you take physical damage that doesn't exceed your armour you still take Stun. For me that is awesome. I am, however not a fan of the BP system as I liked the priority system a lot. But I can see where a change is needed.
For me in general things just come down a fear of change...lol