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.
Yes, I saw that they were making some small changes to the R3 for 2019. I plan on trying the "new" seating position at the dealer's asap, but I don't expect it will be all that different. I haven't sat on a Ninja 400 as yet, but if the seat "slopes" like you say it will be an instant turn-off. Perhaps the optional "higher" seat available will help. It's a real pain wanting to like a bike so much only to be disappointed once you throw a leg over it, but having a 34" inseam and loving small displacement bikes doesn't always work so well. Sometimes I feel like I should just give up and get myself a nice MT-07.