Both bikes that you have shortlisted will be excellent companions for your long daily run. Both the Honda CB350 and Royal Enfield Hunter 350 have smooth, torquey engines, upright seating ergonomics and a plush suspension setup. If you are a taller person, you may feel a little more comfortable on the CB350 because it is a larger machine than the Hunter, although the RE isn't exactly cramped. 

In a similar price range, you should also take a look at the Hero Xpulse 210. With its long-travel suspension, peppy engine and commanding ergonomics, this could possibly be the most comfortable bike to tackle long distances every day. Its seat height - at 830mm - is on the taller side, but if that's not a dealbreaker, we'd strongly recommend taking a look at it. 

A test ride of these three will help you decide which is the best option for you. 

Between the Royal Enfield Classic 350 and Meteor 350, the former would be our recommendation. The Meteor's feet forward position will transmit more jolts to your back over bad patches of road. Therefore, it won't be comfortable over long stints in the saddle. The Classic's upright and neutral rider's triangle will be easier to live with on a day-to-day basis. 

You should also take a good look at the Honda CB350 models because they have a similar riding experience to the RE 350s. But are much lighter and come with alloy wheels and tubeless tyres. They also have a slip/assist clutch, resulting in little effort when operating the clutch. 

Since you are a taller person, looking at an ADV like the Hero Xpulse 210 and TVS Apache RTX 300 is also a good idea. Of the two, the RTX is the better all-rounder, but the Xpulse is lighter.

Take a test ride of these bikes so you can decide which is a better fit for you. 

Since you have a long commute and you want a sporty-looking bike, the options you should be looking at are the TVS Apache RTR 200 4V, Bajaj Pulsar N250 and Honda CB300F. These are machines that will return respectable fuel economy, have enough performance and comfort to tackle your long daily commutes and also be reliable in the long run. 

However, since you have mentioned that your route has a lot of bad sections, we would strongly recommend you take a look at the Hero Xpulse 210. With its upright ergonomics, long-travel suspension and smooth, tractable engine, this will be the most accomplished bike to handle your daily runs. 

Take a test ride of these bikes to see which one suits you best.

Considering your requirements, the options we would recommend you take a look at are the Bajaj Pulsar N250, TVS Apache RTR 200 4V, TVS Ronin, Honda CB350 and Royal Enfield Hunter 350. Of these, the lighter 200s and 250s will feel more agile and have better fuel economy, while the heavier 350s won't feel as agile but will be a little more comfortable. 

Another option worth taking a look at is the Hero Xpulse 210, which will be the most comfortable of all the bikes listed here. However, it won't be as agile owing to its large 21-inch front wheel, soft long-travel suspension and long wheelbase. 

There are also some instances of engine issues being reported online, so it would be advisable to wait for some time before purchasing the Xpulse.

A test ride of these bikes should help you figure out which is the best option for you.