If you have been keeping up with Slic3r, I don't think there are any HUGE surprises. If you haven't looked for a few months, you may find it a much more mature, stable and feature-rich environment than you expect.
I'm not going to go into everything, just a few things that I am excited about and a few that bit me today. For a better rundown, see the blog post here: http://slic3r.org/blog/new-stable-1.2.9
You should go get it.
One feature which I have needed FOREVER is XY Size Compensation on Print Settings. This allows you to fine tune your slicing to produce proper dimensions on your printed objects. Without this (for years) I have spent dozens, perhaps 100 hours and bunches of filament printing test pieces, tuning the size of holes and other pieces, to get them to fit properly. Just yesterday I printed a piece to fit on a motor drive spline, and though my measurements were correct, the thing didn't fit. I did some measurements, put -0.2 into this field, and immediately got a properly fitting piece. This is going to save me MANY HOURS of frustration and printing.
Here's a sample printed at -0.2 (which makes it correct) and +0.2 (which makes it worse) to show what's going on. Basically what happens is that without this correction, Slic3r is underestimating how far out the plastic from the nozzle squishes, which means the plastic area is a bit larger, which means the holes are a bit smaller than required.
One thing that changed at some point in the past (I think) and I didn't realize it until I started using it heavily in the last day is how the user interface has changed. I had been using it in a really idiotic way, just manually changing all of the stuff whenever I wanted things changed. This worked OK as long as I was dealing with a single, one extruder printer, but now that I have a couple of printers and one is dual extruder, Slic3r's new method makes way more sense.
Basically you go into the tabs and set up profiles. You can set up profiles for different printers, different filaments, etc. Then when you go to the first tab (the plater), you just select the profiles you want to use:
Once you get your profiles set up, this makes it much easier and more foolproof. I've wasted a lot of time and plastic because I forgot to change one thing in one tab. This breaks it down into just a few profile selections to get everything right. Until I figured this out, I was struggling a bit. Now it's easier than ever. As always, learn your software and use it the way the author intends, or pay the price in time and frustration. Or, you know, write your own software if you don't like it.
One thing that I'm missing - on the File menu, according to the docs, there's supposed to be a "Combine multi-material STL files" option. I know it used to be there, I used it once over a year ago. It's gone. I don't know if it's intentionally gone and they haven't updated the docs, or it just got omitted. I can work around by putting both objects on the plater and manually aligning them, then manually choosing different extruders for the two objects, but the ability to make an AMF file to get all this done was nice. Maybe my "workaround" and then exporting an AMF is what we're supposed to do now. If so the docs need to be updated.
One thing that's not new that I should warn you about: when you upgrade Slic3r, I would HIGHLY recommend killing your configuration and starting over. Slic3r has a bad tendency when you upgrade versions of getting really wacky if the old configs are still there. I spent HOURS yesterday with things not showing up on the dialogs for dual extrusion, and with one extruder badly underfeeding. Eventually I got on IRC and LoH showed me a screenshot of what it should look like, and suggested deleting the config. FYI the config on Windows is in C:\users\(name)\appdata\roaming\Slic3r - I'd suggest renaming that to something like "Slic3r-hold" then restarting Slic3r and letting it build new configs.
Here's a before and after of a dual extrusion attempt. The "before" is when for some reason Slic3r was under-extruding by about 95%: