Which bike or scooter should I opt for

I am providing you the detailed specs of the three bikes selected by you.

Engine & Transmission specifications
Honda CB Shine has the greatest engine displacement in the list provided by you whereas Activa has 124 cc engine displacement and discover has 124.6 cc engine displacement.
The power generated by Honda Shine is 10.57 Bhp@7,500 rpm, Activa generates 8.50 Bhp @6,500 rpm and Discover generates a power of 10.80 Nm @5,500 rpm. The gearbox type is manual in Honda Shine and Discover whereas Activa has Automatic gear box.

Brakes,Suspension & Wheels
The Brake type is Disc in CB Shine SP and Discover whereas Activa has Drum type. The is Front Disc in Shine and Discover only. Rear Disc is not available in any of the vehicles.

Dimension and Chasis
The Kerb Weight of Shine Sp is the highest i.e. 124 Kg then discover has 121 Kg weight and Activa has only 111 kg weight. In length Discover stood first then shine and after that Activa. Discover has the greatest ground clearance 160 mm and Activa has the lowest Ground Clearance i.e 155 mm.

Fuel Efficiency
This specification is often considered as the deciding criteria. Shine has 10.50 Ltrs Fuel Tank Capacity, Activa has 5.30 Ltr and Discover has only 8 Ltr fuel tank capacity.

On Comparing Mileage Discover is giving 82 Kmpl whereas Activa just gives 54 Kmpl and Shine has a mileage of 65 Kmpl

Price (Ex-Showroom ,Mumbai)
Honda CB Shine SP (CBS BS IV)
Price Rs 66.244

Honda Activa 125 (Std. Alloy BS IV)
Price Rs 60,541

Bajaj Discover 125 (Disc)
Price Rs 53,264

Yes,GST Will affect the price of the bikes. After 1 July the Ex-Showroom price will become same. You'll be charged additional 3% cess if you are buying a bike whose engine size is more than 350 cc. The spare parts price and maintenance price will get affected by GST and Also the price of bike will be little increased by GSt but that would affect so much.

I should suggest you to go for Honda Shine SP as the handling,looks and mileage all are good. This bikes looks more attractive and has achieved more awards in the segment.

In the two wheeler market there are many big players, Honda, Hero and Bajaj are some among them as already sorted by you.

As per specs Honda seems to be quite attractive though it's prices are slightly more than the other brands in market.

If you are concerned for running cost then Honda Discover will be a good choice.