I'm really happy with my SE, though I wonder now why I waited 9-10 months to install the TRD rear-sway-bar on it, seeing how it really is a very noticeable improvement in handling and stability. Yet another thing that should have been standard equipment on the SE, even if it raised the selling price by $200. It does sort of bug me that Toyota isn't willing to invest a bit more performance "street cred" into their SE/Sports trim models from the factory than they do.
Some people have complained about the low-speed turning radius penalty that the "Sports Tuned Steering" imposes on the SE, but it's a fair trade-off for the improved handling/responsiveness on the road IMO. Of course, that is something that everyone has to decide for themselves. Same with the "Sports Tuned Suspension" in term terms of performance delivered versus ride quality sacrificed. The ride can be somewhat harsh on lower-quality, choppy roadways, but is smooth, quiet and comfortable on a good road/highway.
Braking with the 4-wheel-disc-brakes is top-notch, and the car really does feel like it can stop on a dime (though can be sort of catchy at low speeds until you get used to it). I read that wind/road noise dampening is improved over earlier models, but that is something you will need to compare for yourself, as I haven't driven anything earlier than a 2015 model. Same with increased body rigidity via more spot-welds on the frame of the 2015/2016.
I'm not sure if you prefer automatic or manual, but the clutch on the 2015/2016 is of a new hydraulic design for the Yaris, and said to be a big improvement over the earlier clutches for the car. I really like it, though it feels longer (more travel from full depression to release) than the Honda clutches that I have driven in the past. The automatic is the same tried-and-true bulletproof one that has been in every Yaris since it debuted.
The upgraded seats in the SE are also very comfortable and grippy, and keep you in a good driving position on hard/fast cornering and such.
If you have been happy with your 2008 RS, then you will probably also enjoy the 2016 SE, as the car is extremely similar mechanically, with only minor tweaks here and there to differentiate it from it's earlier brethren. The cosmetics/sheetmetal really is the biggest difference in the 2nd and 3rd gen - and that all boils down to subjective opinions. Personally, I like BOTH from an aesthetic standpoint (including the 2007-2012 sedan/Belta version of the car) - most notably in the SE/RS (3rd Gen) and S/RS (2nd Gen) trims.
Happy hunting!