I sat on an R3 at the dealers and got the same "sitting in" sensation. I also instantly noticed the slope, something I absolutely hated on my Ninja 250R. With a 34" inseam the pegs also seemed a lot higher than the CBR's.
I think I'm just a tad too tall for an R3, which was a little disappointing because my first 2 bikes were Yamahas and I'd love to get back on one.
I'm dragging my feet on the Ninja 400 hoping that sales figures will convince Yamaha to jump in and market a 400 as well, hopefully with a slightly higher seat and lower pegs than the R3.
It looks like Yamaha are committed to the 321cc motor for the foreseeable future. Have you seen the 2019 R3? Yamaha have dropped the handlebars and replaced the instruments with a TFT display, and not changed much else. One local dealer did offer me a new 2018 R3 at over 20% off list but it was the matt black colour which I think looks awful. Too much like a bike that's been thrown down the road a couple of times and hand sprayed by it's owner to try and make some kind of nihilistic statement. If I could have had the blue option at that price........................
I rode a Ninja 400 last year and whilst it was a pleasant enough ride it didn't inspire me to open my wallet. As far as I can remember the performance didn't feel much different to the R3 but then both are built to satisfy the European A2 licence requirements which stipulate maximum power and a maximum power to weight ratio. Also, there is very little in the way of luggage options available for the Ninja and the seat is rubbish, too slopey and just not bottom shaped. Well not mine anyway.
I've found a bike shop about an hour's ride away that offers a seat reshaping service using memory foam inserts. So if they can scoop mine out a little at the back and build and up broaden the front to flatten it and give a little support under my thighs like the CBR250R did then that could be money well spent. As it is the R3 seat's not terrible but could be better.