Like pretty much everyone here has already said: you owe it to yourself, and even more so to your 'better half', to go and seriously test ride both the RT Ltd and the F3 Ltd. Just be sure to compare the RT to the new 2017 F3 Ltd. for the truest comparison overall. The newest F3 has both the integrated backrest/topcase as well as automated rear suspension; that makes it more truly comparable than other F3 variations. The real difference, then, is between the ergonomics of the two bikes.
We recently went through the exact same mental wrestling match trying to choose. In our case, I first thought we would likely opt for an RT when we went to look. How wrong that turned out to be. The seating on the RT was painful for my hips; much less so on the F3. But, we did the RT test ride anyway, and enjoyed it enough to want to try more. The dealer pulled a brand new 2017 F3 Ltd out of a box and put it together; two days later we tested it. I felt much better in the driver's seat of the F3 Ltd than the RT Ltd. My wife enjoyed the ride on the F3 Ltd passenger seat somewhat more, as well, in spite of the breeziness. She loves the open air and sporty feel. Her opinion was that the RT felt "too big", and that the F3 Ltd was more what we would be happier with. I didn't argue.
In the end, it really is a personal choice, and should depend on how both of you feel, physically and emotionally. On the F3 Ltd, I can change the position of the driver floorboards, and likely will soon try a switch from position 3 to position 4. The passenger floorboards are not adjustable that I am aware of. I'm also going to do something about the F3 stock driver's seat. While my hips feel better than on the RT, the stock F3 Ltd driver's seat is uncomfortable for me after 60-90 minutes. I will look at a Day-Long or Ultimate as a swap. My wife, though, is quite happy with the stock passenger seat on the F3 Ltd. She even feels secure enough that she wants me to remove the arm rests that I had installed for her added safety. Probably also will opt for a larger windshield, possibly an F4, to cut down on the breeze. She doesn't mind the wind, nor do I, but my senses tell me we would be better off with slightly less buffeting. However, I don't want to entirely lose the 'sporty' feel of the F3 Ltd, either.
We bought our F3 Ltd to basically do two-up riding; shorter day trips, maybe an overnight or two. We won't likely do long distance touring. We've so far done 7-8 hours (300 miles round trip) in a day, and several 3-4 hour day trips (with a couple of breaks). That's also a factor in your decision-making. There's no need to rush; plenty of Spyders available. Do your homework; keep testing. Listen to what your bodies and your instincts tell you. Then choose one, and have yourselves a lot of fun.
Your money; your decision. Choose what suits YOU and YOUR NEEDS, not because of what others have done. If any of our experience is helpful as a 'guide', it is freely offered, but very much subject to whatever value (or not) that YOU wish to give it.
