So, it depends upon how much you insist on having the rules pre-scripted and how much you're comfortable flying by the seat of your pants. All three of these approaches are entirely valid ones. It's just a question of what it is you're looking for in a game.
If you're the sort of GM who wants to have everything spelled out, with every "i" dotted and every "t" crossed, then just run 'em using SR2. There are changes between SR2 & SR3 that will change the look and feel of things if that's extremely important to you. (The Skill Web & Grounding are the first two major differences that come to mind.)
If you're the sort of GM who's comfortable with a little lee-way, but you can't imagine Shadowrun without Combat Pools and variable target numbers, then you might want to try SR3. SR3 cleans up a lot of things from SR2. Magic, Decking, and Combat are all still pretty different systems. However, the SR3 implementation of them is a whole lot easier than trying to decide if you want to use the rules out of the SR2 core book or the rules out of VR2. (et al)
If you're the sort of GM for whom the rules are a nice starting point, but ultimately, you feel that they're just there to sort out the random factors in the storyline, then you'll probably want to switch to SR4. For most people who haven't thought Shadowrun in a while, the SR4 system is a little more intuitive to pick up. However, the stat-lines you see in any SR2 book are going to have a very different effect in SR4. The basic attributes have changed and the values of skills have changed as well. (A character who depended upon a 6 skill in SR2 might only have a 3 in SR4.)
For some scenarios -- e.g. Universal Brotherhood -- that wouldn't be a huge problem. There are stats for Insect Spirits in Street Magic. So, you wouldn't need to convert them. For other scenarios -- e.g. Harlequin -- it'd be a bigger problem. Unless you're really flying by the seat of you're pants, you'd probably want to take the time to re-stat a number of key NPCs. There is a
character conversion guide that's freely available. So, that'd help. However, you still might find yourself going through it several times for each scenario.
The wireless matrix vs. wired Matrix is really more of a paradigm shift than anything else. The hacking rules from SR4 work perfectly well with a wired matrix. They're an abstraction, and you just have to accept that first.