I have a Ninja 500R and find riding for 4.5 hours on one day very easy to do. (It's only 16% heavier than the Ninja 250(R).) I use the OEM seat - some people say that you "have to" buy an aftermarket seat from Corbin, but I honestly don't see any need.
First of all keep in mind that EVERY motorcycle is uncomfortable for travelling compared to a car. (Even if you get a Goldwing with giant fairing, giant windshield, radio, heated everything, and so on.)
Second, keep in mind that the Ninja 250(R) isn't really a sportbike - its riding position is very similar to that of a standard motorcycle. Some people will say that a cruiser is more comfortable but I'm not sure whether that is actually true - if you have back problems for instance, a standard motorcycle would be possible, but a cruiser would be very painful.
With a motorcycle, a lot depends on your body - how long is your inseam, how long are your arms, how do you like to sit, etc. Because of that, it's very difficult to recommend a specific motorcycle - I would try out a few motorcycles and see for yourself which ones you find comfortable. Have you also had a test ride on the Ninja 250(R)?
Here are a few that I think you should check out in addition to the Ninja 250(R):
- Suzuki GS500(F): the GS500 (no fairing) looks like a streetbike, the GS500F (fairing) like a sportbike
- Kawasaki Ninja 500R
- Suzuki SV650(S): the SV650 (no fairing) looks like a streetbike, the SV650S (fairing) like a sportbike
- Suzuki LS650 Savage: cruiser looks
- Honda CMX250 Rebel: cruiser looks
- Yamaha Virago 250 or 500: cruiser looks
- Hyosung GV250: cruiser looks
- Hyosung GT250(R): the GT250 (no fairing) looks like a streetbike, the GT250R (fairing) like a sportbike
If you are planning to use a motorcycle for travelling I'd also recommend to look into luggage options BEFORE purchase. I'm a bit paranoid which is why I prefer a top case over soft bags - and on some bikes there are no top case racks available, or they require modifications to the bike. Because of that, think about which luggage options you'd prefer, and then check out which ones are available for which bike. It can be difficult to mount a top case or side cases on some motorcycles, especially on sporty looking ones.
Also, pay attention to wind protection - at speeds of 50mph or higher wind starts to get annoying, and the type of fairing and type of windshield make a big difference. I for instance find the wind a bit annoying on my Ninja 500R - on the Suzuki V-Strom 650 I don't even notice it. Again, that's something that you have to pay attention to during your test ride - make sure to take it on at least a rural highway (better a freeway) during your test ride to check wind protection.