Here's the thing I've decided after my first two bikes: The highway is just not going to be fun. You could compromise further and further toward something more comfortable for the highway (it's not just as easy as "bigger") but you're potentially impacting the bike in those slow speed / urban environments and spirited windy backroads / weekend track events. You'll always get batted around by double-trailer semi-trucks and strong wind gusts. (A full-fairing bike would be better in this regard.)
I took my CB300F on a few long trips (including one 1,500+ mi) and yes, it's strung out doing 70+ mph on the interstate. But doable and, I think, totally fine for the little single-cylinder thumper. I also regularly did 45 min - 1 hour stints on the highway regularly (to get to better backroads). And shorter stints to get around the city. Not problematic.
I'm 5'11" and had been ~175 lb range. Some people might look at you on the small bike on the highway and think you're nuts. But there's ample acceleration even at highway-plus speeds. Your hands will get numb from the vibration. You'll have tons of fun around the city and on curvy roads.
I thought my Suzuki SV650X would be better on the highways -- it is, but not hugely, as much as I might have thought beforehand. You're still in an awkward position relatively speaking that you can't change, focusing 100% of the time because it's not a car, getting blown around by the wind, waiting for your destination. And hopefully you remembered the ear protection or your head will be ringing afterwards. But it's hugely entertaining around the city and on the backroads. The sub-1 hour trips on interstates (posted 65-75 mph around here) are, indeed, more tolerable and they go by quicker.
The CBR300 on paper is the better bike than the CBR500. But the 500 could certainly fit someone's riding better. A few problems are, as you noted, there's a much better supply of 300s, and there are also some great bikes to be had competing at the 500's entry point (like the SV 😇).