I was questioning the same choices of bikes. My previous (still in the garage) was a 2007 R1, far from stock, Brembo HP brakes front/rear, BST wheels, Ohlins all around, BrakeTech CMC rotors, AIM MXL Pista dash, Bazzaz TC, etc. Dream to ride, but I wanted something newer. As others have stated, go to the forums of all the bikes, and you will most likely get answers for that specific bike, and a few that are haters that will tell you to go away, say 90% for, and 10% to get something else.
When I shopped, I looked at the R1M, Aprilia RSV4 RF, 1299 S, BMW S1000RR, BMW HP4, and a few more. I really wanted the R1M. Sound is killer for it, and I liked my Yamaha before, been rock solid. My BST wheels wouldn't move over to it, so that was a kick in the pants, so I branched out and looked at the other bikes. I have ridden them all, and my wife now rides an 2016 Aprilia RSV4 RF.
The R1M, I couldn't get it, nearest one was 300 miles away when I was looking, and they didn't want to move on the price. They were asking a premium for it, and I wasn't going to do that. I rode a buddies, and it felt good all around, handled well, and my only complaint were the brakes. After an aggressive run down a 40 mile twisty road, the brake were fading a bit. He even had swapped the fluid and put different pads on, but it was still having a bit of fading (could be me being used to my CMC rotors/Ferodo Pads, but it was still noticeably different at the end of the road compared to the beginning.)
RSV4, I liked it, I looked at the 2014 model at the time, it did everything I wanted, except the dash just felt old. (2017 mode... totally hot, and I maybe would be riding it if it was available at the time). It handled well, and the power band was VERY similar to the 07 R1, really liked high revs, a bit of a dog down low, but felt great. A real beast winding it out in the RPMs, and just giving it hell. The smooth top end power just pulled, felt like a rocket up top, brakes and suspension felt good too.
BMW, I'll lump both the HP4 and the "standard" in the same group. It's an i4 motor, felt great all over the rev range... but they are ugly. Looks like someone slapped it upside the head and gave it a black eye. I had found a lightly used (700 mile) 2013 HP4, and was looking at the 2015 S1000RR. I rode the HP4. Just felt amazing. Really did. Handled awesome, felt no issues with brakes, just all over felt phenomenal. The S1000RR was right there with it, felt a tad heavier, but the HP4 was the closest I had found to the my 2007 R1 in terms of handling (the 07 R1 weighed 387 pounds wet in street clothes, and with BST wheels and CMC rotors, it felt like a 250 in the corners). The S1000RR was at the top of my list, but did I mention it was ugly. It also was missing character. It was great all over... but it just felt sterile, normal. I felt I could easily go fast on it, it wasn't going to kill me, and could be a lot of fun, but it was just missing something, like eating the same food for every meal... I felt it was going to get old and I'd have to keep tweaking something on it to make it special.
I rode my 2015 1299S. It felt similar in weight for handling to the HP4, but was "smaller" overall. Mid-corner, I didn't like the feel of the 1299, corner entry was fine, but felt heavy "holding" in the corner, so much, that I actually stopped and checked tire pressure. Power... I felt it was just lacking. I keep riding it and questioning why it felt so down on power, then my wife chimed in on the Sena headsets asking "are we in a race, you keep leaving dark marks coming out of the corner and blasting it". The power was there, but it didn't have any "bang we're on a rocket ship" moments like the RSV4, S1000RR, and my old R1 (anything under 8k RPM was a dog, but above 8k, it was a rocket). I quickly figured out, the torque and power of the 1299 is just there, it's anywhere in the RPM range, it just freaking pulls. With that said, I hit, and still do, the rev limiter all the time, it just doesn't rev like an i4 or a v4 does, but man it pulls. And it's freaking sexy. Like super model out of Leo DiCarpio's league sexy. I also did NOT like the 1299 S at first, and even posted up a long explanation of it, and finally after moving my CMC rotors to it did it finally get rid of the mid-corner weighted feel, and felt like I was riding something lighter and better than the 07 R1.
So, for me... all the bikes had ample power, ample handling. I have a Ducati, BMW, and Yamaha dealer close, so support isn't an issue. Now the Ducati dealer does Aprilia and MV Agusta as well. So really it came down to this question:
Which gives me the bigger chubby...
I liked the look of all of them, except the BMW... still can't get over that front end. Riding comfort, all felt similar to me, comfortable enough for 300 miles of riding in a day, or the track without any changes, still going to be sore riding any of them. The R1M looked good, but it was only available in blue, and well... all my gear is red/white/black. Didn't really match well. The RSV4 I think is sexy. But... the 1299 S... just something to lust over, and saying, "I own a Ducati" is something that people get, they know the brand, they know it's exotic, there is something about the ownership of the name over the others. The 1299 S gives me a chubby, I ride it, and I smile every damn time I twist my wrist. The Akra exhaust screams, and the front wheel wants to come up and I am gone. I see it in the garage and I just smile. I clean it, I smile. I work on it, and I smile. Really the ONLY time I don't is thinking about how much money I have spent on it, then I look at it, ride it, and say, "What gifts can I buy you..."