I can't really say what's
BEST, other than mirror what other people have said which is "Play whatever your table enjoys". I won't break down the minutiae of the rules or pros and cons like others have done(they do it better anyways), but I'll give my honest impressions on the editions I have played/GMed though:
1E. Never played, but I read most of the books(I'm a nostalgia and lore junkie). I can definitely understand how people felt the rules were clunky. The setting was great but a tad restrictive(limitations on magic, cyberware, etc), but the metaplots and atmosphere were incredible.
2E. BIG WORD DUMP AHEAD. My group recently started a campaign in this system, so I've read most of the books a few times. Previously we did a 4-year 4E campaign, thoughts on that below. So we decided to do a classic 2050s game, and it made sense to use a classic 2050s system. While the rules are definitely a touch clunky at first, and compared to later, smoother systems, I'm honestly amazed because the mechanics are so intrinsically tied to the lore of the setting, and they reflect that. Example: Various augmentations have different rules for how they interact(or don't) with other pieces of ware or modes of operation, and they go into a little detail about why that is. Like how a Rigger datajack and a Decker datajack use different spots and function differently because they interface with different parts of the brain. Very cool.
The atmosphere of the world improved even more, and it truly felt like the best expression of the cyberpunk "Man Meets Magic Meets Machine" that we know and love. The metaplots continued from where they were introduced in 1E, and things ramped up a ton along certain major plot lines(
Universal Brotherhood ->
Bug City, being an obvious example). It is quickly becoming my favourite of the editions I've played.
3E. Again an edition I haven't played, though I read about half of the books. Mostly lore and plot ones, as the rules books aren't a priority unless I plan on switching to 3E at some point, which I'm not right now. If you look online, you'll find people are very split on 3E. Some people love it, and swear it felt like the ultimate evolution of the rules and system that began in 1989. Other people feel very strongly that it began to change too much, dilute the atmosphere, etc, and they stuck with 2E as their preferred system. Neither is right or wrong. Story wise, more great metaplots were introduced, though this edition definitely felt(to me at least) like it started a lot of new plotlines instead of just continuing existing 1E or 2E ones. However, they're no less iconic or riveting. And sometimes terrifying. Just ask any veteran players about Medusas.
4E. My original Shadowrun experience, where I played for about 10 months in a friend's campaign before running my own for 4 years. As such, I do love this system, and it feels very complete to me. IMPORTANT NOTE: We technically played SR4A(the 20th Anniversary Edition, basically 4E but errata'd). Also a very divisive edition depending who you ask. It turned the setting on it's ear a bit by trying to modernise the universe that was inspired by 80s cyberpunk. It introduced wireless networks, streamlined and expanded bioware and nanite-based systems, had more info on space stations and metaplanes, and honestly it felt the most Science-Fiction of all the editions. Which honestly isn't a bad thing exactly, though it definitely took the gritty, street-level game of 1-3E and basically made it Shadowrun-But-Shinier.
The story and metaplots started to focus on magic and BIG events a fair bit. Maybe it took inspiration from
Bug City, Renraku Arcology: Shutdown, and others, and saw how popular they were. There was a lot of plot around a war in Central/South America(think Neo-Vietnam for flavour), and an entire Dragon Civil War and culminated in not 1, not 2, but 3 MAJOR PLOTS involving the big upright iguanas. It also set the stage for metaplots to come, but that's basically been a tradition since forever with Shadowrun. Mechanically, it changed the system the most radically, and a lot of the rules it introduced are ones still used in 5E. Had a couple issues with things like massive dice pools, and I feel it catered to Powergamers the most out of all the editions. Still really damn good overall though.
5E. Hoo Boy. The controversy continues, and you'll understand why in a bit. But first off, 5E is a product of what the designers tried to do to fix some of the more glaring issues with previous editions, and still retain that old-school feeling from 1-3E. Grittier, darker, longer shadows, but no clunky rules. They tried, they really did. And despite what some people may tell you, they somewhat succeeded. I played a 5E game for about 8-10 months off and on, and I've read almost all the books that have come out(except the latest couple I think?), but I've stayed pretty up-to-date with what's going on with the game, CGL, etc. So that's where I'm coming from with this.
BTW, I will NOT just be shitting on 5E here. This is my own opinion about the way I feel about the game I played, and what I think of it as an edition. I'm mostly positive-ish, but feel free to check out other opinions here and on places like Reddit and Dumpshock(just bring a lime and some tequila if you do, because there's a lot of salt).
The surface rules mostly make sense, especially as a narrative tool, though there are a few glaring contradictions and rules confusions in need of errata. It primarily uses the rules introduced in 4E, though it tries to fix some of the issues of that system with moderate success. I won't get into the compplaints some of the other people will inevitably bring up, so I'll simply say 5E is pretty fun as long as you're okay with using a little GM Handwavium if you come up with rules that seem confusing, contradictory, or absent. Roll what makes sense and feels right. One thing I will note is 4E and 5E both tended to separate rules from fluff a lot more than 1-3E, in that the lore explanation for they way things worked isn't always reflected in the rules. Synergies between augmentations are mostly gone, though they still note conflicts(EX. 2 pieces of ware that won't work together).
Atmospherically, the setting seems in conflict with itself a bit. On the one hand, it returned to the darker, street-llevel roots in a lot of ways. The Great Big Metaplots were still there, but it was coming at you like you were mucking it up with the rest of the Runners. Jackpoint seems a little more open and grounded in 5E, whereas in 4E it seemed almost like the members responsible for the infodumps(and in-universe lore) were more removed from regular Shadowrunners. And this is good, I like the flavour in the books of 5E a lot. However, the setting's focus on magic gets VERY significant boost, to the point where technology and mundane stuff honestly feels like it's the forgotten 1st child and magic is the new baby that gets all the attention. I don't know the exact ratio of magic-focusing(or involved) splat books to non-magic ones, but the universe of 5E sure feels more fantasy than previous editions. This isn't...bad per say, but it does feel like there's some balance issues. Maybe this is what all the Die Hard 3E players felt like when 4E introduced Wireless and was so tech-focused. Huh. Interesting.
6E. IT'S NEW AND SCARY, RUN AWAY! Okay seriously, I know as much as most people here, which is from checking out the preview and podcasts and Shadowcasters Network and whatnot. So with excitement(and a little apprehension, to be fair) I'll keep an ear out.
