If you are going to take a pillion , check the load ratings of the bike.

For comfort, A smaller 250 mini adventure or a street scrambler type bike (edit. Maybe a 250 maxi scoot) might suit you better than a naked sports like MT25 or z250.

The caveat is, whatever is comfortable, and has higher load rating, may quite easily run into tradeoff in terms of city maneuverability...

Consider the KTM Adventure 250 if pillion comfort is a concwrn or a Bajaj Pulsar NS200. You can also try the Honda CB250 but that's hella expensive for a 250cc naked single cyl bike. Very comfy though if I weren't limited by budget and the fact that its stupidly expensive for what it offers I would probably have bought it.

Or you can always get a 250 scooter but the price will be significantly higher both to buy and to maintain. Fuel consumption is also significantly worse than a bike with hand clutch/centrifugal clutch.

Anyway, 250cc is a bit limited.

Comfort is a basket case of attributes like sitting position, frame size (ie. means longer more spacious seat), wheelbase, vibration etc. As you can see some of which means it may result in a bigger and heavier bike, which may impact on maneuverability.

For bikes, as was mentioned, the KTM 250 Adventure. However, this bike has a relatively tall seat height. but if you have the legs for it, its a good candidate. The Versys 250 is a bit easy to manage...and probably the best of the bunch owning to the same 250 twin out of the ninja and z250. Other bikes in the class is the TRK 251. You may see the Vstrom 250 sometime in the future.

for 250 street scrambler type bikes, you are basically limited to a host of chinese bikes, which may or may not be your cup of tea.

What you can do is try out the new CFMOTO 250 CL-X, Leoncino 250 and the TNT250 sports naked. They tend to have a better or more generously proportioned pillion seat compared to a MT25.
Modenas may launch a 250 Pulsar or Dominar sometime in the future as well.
Best for comfort will be a 250 maxi scoot. But bear in mind, they can be bulky, heavy and long. But for comfort, they are unmatched.
But if you are on any of these, dont expect to cilok like a kapchai.

after so many different suggestions and can see you are still fond of slightly upright seating position 250cc bike ( e.g: KTM Adventure 250 and Vesys X-250 ). Perhaps you can follow your heart. Knowing your buying patents ( eg: car you own ) if you will change / upgrade motorcycle quite often then I would suggest you to go for 2nd hand bike first. Japanese 2nd hand bike won't have much of issue, just need to check whether the chassis / frame, wiring, engine, gearbox, & etc in good running condition.

It will safe you a lots of money and also understand what you want is what you need.

me 2 cents.

And so is Benelli.

If you are not looking at Chinese bikes and scooters ...you have definitely pigeon holed yourself.

You can't buy a new versys 250. Because there are none....until modenas decides to bring them in again.

So that leaves the KTM. But if you are worried about parts and reliability, you are pretty much left with no candidates. Small displacement KTM are coming out if India, while the bigger 790 is coming out if china.

There are no problems with parts for modenas/Bajaj bikes. Basically they are the poor man's KTM. (Yes you read that right. Bajaj makes KTMs). But judging from your preferences, the Bajaj based bikes probably aren't for you either.
If based on your initial preferences of a city bike with comfy seat, only a scoot fits the bill. Even a small adventure bike is big  if your previous experience is a 100kg kapchai, any of the 250 ADVs and maxi 250s will be close to double that.

The closest 250 scoot that fits your bill would be the ES250 scoot..but that being a Chinese bikes and a scooter...no dice.

Bajaj Pulsar is Indian being sold in here as a rebadged Modenas bike.

Yes, you will run into some QC issues (typical of India manufacturing, made worse by Modenas) but spare parts and maintenance in general is dirt cheap. In my experience, I have had the rear brake go kaput right out of factory, rear pillion seat not being able to lock up tight, and minor fork leaking, all of which can be covered by warranty or you can fix on the cheap for less than 300 if you wish to avoid DRB-HICOM's warranty shenanigans. If you are careful you can get to Penang mainland on a single tank from Petronas at Sg Buloh Overhead Bridge.

If you don't want a Yamaha FZ150 or just want the cheapest ABS bike you can buy, this is pretty much the most economical alternative. As long as you are staying in Klang Valley there are several specialists covering key areas, the ones I know are in Kota Damansara, Selayang, and Puchong Prima. There are other normal service centers that service other bikes like Eang Chun in Wangsa Maju that will keep spare parts for the bike as well.

KTM ADV 250 is heavy, you are approaching 180kg with that thing and is tall, but is plenty comfortable. Price however will make your wallet cry and costs just 1-2k below the Honda CBR250RR.

Personally have never tried Versys 250 so can't say anything about it other than it shouldn't give you any major issues, considering its based on a very old reliable Kawa design.

Another alternative you can consider is to buy a used Kawasaki Z250 and modify the rear seat to have better padding.