what is the tyre pressure you're using? This is one oft neglected aspect by two-wheeler riders. The right tyre pressure can make your ride more comfortable and will also reduce wear and tear on the bike. Check this for the ideal pressure: Tyre Pressure for TVS Wego (24-32psi), Tyre Air Pressure . This is what I used to keep on my TVS Jupiter as well, which has the same size tyres.
Additionally, scooters like Wego, due to their smaller tyres (12"), tend to respond more to potholes. Bikes have bigger tyres which tend to be more comfortable. For instance, Honda Shine has 18" tyres. Of course, driving them is slightly more strenuous, at least initially. So take your pick.
You might also want to familiarise yourself with your regular route. When I drove to work regularly, I knew every pothole that I would encounter and had learnt to avoid them. If you have to drive on unfamiliar roads often, you might want to drive a bit slower and avoid overtaking to reduce the chances of encountering potholes.