First of all please advise on which routine you are driving your bike? i mean in short run with rushy areas like some androon shehar type routes or your daily drive is on long routes?
further i can say any thing after knowing the answer...
On a common note:
I am not much satisfied with Suzuki workshop mechanics for tuning especially. They have charged 475PKR for tuning and just check:
Tappets, filter, chain, plug, and penalty of WD-40 spray where they easily can. They don't bother even to check other things.
Alhamdolilah I have GS 150 SE and it only used for touring, its milage is 7500km. I don't share my bike and never use it in city. but i am tuning it by my self twice a year with full tuning which includes each and every thing as per company standards.
Please get a feeler gauge and adjust your tappets accordingly,
Wash the filter as directed in book and let it dry and then use mobil oil on it as advised in book.
Carb setting if unadjusted by some mechanic then tune it or better to complete wash it with some carb cleaner thoroughly.
Check you drum bush and adjust the chain. (Lubricate the chain with industrial grease of best quality)
Clean you plug with needle or with brass brush by applying any cleaner.
Please also check the wiring nodes/ terminals and de-rust them.
Your tyre size must be as per original size.
Please also calculate the electrical load, if you have installed any after market items on it.
Remove the breaks switches and replace these with some good quality switches in market.
Please make correction, CG 125 is giving that much vibration in handle as you explained, i have 2 honda cg 125 Alhamdolilah. One of them is restored by me and its also have not that much vibration.
Each engine gives vibration which is without shaft balancer. GS 150 SE also not having this balancer.
Inshallah you will feel much better, in ride.