I can't really speak for the 1299 base and the new rsv4 but between my 1199s and my brother's '14 rsv4 factory, I'd choose the Ducati over the Aprilia for the fast street stuff.
Panigale:
+torque/power
+looks
+character/feel
+sensitivity (throttle, brakes, steering, etc.)
+TFT dash and upmarket controls (I'm no technology freak but this stuff is so much fresher and softer on the eyes. Makes a considerable difference since that's what you interact with whenever you're riding the bike.)
+electronics (namely, traction control. RSV4's is too obtrusive in any setting other than the lowest, 1. Same tires, same road, same rider, I have the 1199's set on "3" of 8 and it NEVER gets in my way like the Ape's does even on level 1)
-ergonomics (for a smaller person. The RSV4 strains my wrists and my back less than the 1199)
-heat
-stiffness (yes, that can be dialled out.. but apples to apples)
-Expensive mods and the bike begs for them ($3500 Akrapovic, $1500 DP rearsets, etc.)
RSV4:
+sound
+feels more solid/stable (but less flickable because of the added weight)
+fits like a glove straight out of the box; so much easier to "lock into the tank/bike" (for a smaller person)
+suspension (considerably more plush whilst managing to corner just as quickly, if not more quickly than the Ducati)
+Cheap mods and the bike doesn't beg for them the way the Panigale does. My brother got a race ECU, Akrapovic slip on, tail tidy, and mirror block off plates. Maybe one or two other goodies and called it a day-- all of which cost far less than the price of the 1299 Panigale DP Akrapovic exhaust alone!
-tame inline-4-like power band minus the sound (perfect on it's own but not when comparing it to the 1199. One may have to ride a Panigale like a 2 stroke in stock form, but when it kicks in, it REALLY kicks in. The RSV4 motor is bland in comparison even with the Akrapovic exhaust and race ecu. And not just from idle to the mid range.)
-far reach to the ground but very compact whilst on the bike (maybe you get used to that after a while? or maybe it's a non issue for anyone tall)
-WIDE seat (I complained about my 1199 seat, and the DP Race seat, and the 899 seat... until I tried my brother's RSV4.)
-dinosaur dashboard (they've tweaked the '15 dash, but not enough in my opinion. still feels old)
-headlights don't inspire confidence in the dark (compared to a base Panigale to be fair)
-this is very subjective/opinionated - The RSV4 may have a nice tail piece, and perhaps a few striking lines here and there but... I just cannot stand to look at the bike's Fugly face with the THREE headlights in stock street trim. Especially when parked anywhere near a Panigale (any Ducati superbike for that matter; 1x98, 998, etc.)
Finally, and for the record, this is my own personal opinion, contrary to what the majority suggest...
Panigale throttle > RSV4 throttle
Hands down.
Even with crappy OEM fueling and the throttle slack, I prefer the 1199's throttle over the Aprilia's. And it's not because I am more familiar with my own bike. I would've made the exact same claim on the very first day I tried both bikes, bone stock, on the same road, for the same distance. In all riding modes, the Aprilia's throttle feels more artificial to me. And the low-to-mid range lack of torque doesn't help at all in this regard.
That said, the Rapid Bike module, alongside the Akrapovic evolution exhaust and the throttle spacer kit from Ducati Omaha which I installed on my 1199, all stretch the gap even further in the Ducati's favour, compared to the RSV4 with race map and Akrapovic.
I love both bikes. I wouldn't hesitate for a second to choose the Aprilia over the BMW. I might have to think twice when trying to pick between the RSV and the new R1. But between the Panigale and the Ape...
Ducati 10 -- Aprilia 0
What works for one person, might not work for another. And what works for the other, might not work for the first. That sums up my opinion of the "1199s" vs '14 RSV4 Factory.
In short, for Fast street stuff, I vote Ducati 1299 base.
Best of luck..