I want to run two circuit with 12/3 Romex. Circuit #1 will be 3 light fixtures and circuit #2 will be two GFCI Receptacles. I am concerned about having shared neutral. From reading other post it is advised to splice all neutral and not use screw terminal to connect the two circuits. Also I will not be using the load side of the GFCI receptacles.

Shared neutrals are fine, still very popular in homes, thou a loose connection can cause some problems. Splicing at a device and not using screw terminals is not just wise advice, it is also required by code.

Just be sure any splices up to the point the two circuits split off are good and tight, along with the connections in the panel, and you will not have any problems.

Should I used a Double Pole Breaker. So that if one side of the breaker trips the other side will as well? Also is this OK in a commercial environment?

It can be on 2 single pole breakers.
Unless it is in 1 device. Then both must break.
You do want pigtails, so if you change out device, neutral remains intact.
Neutrals Need to stay together.

Unless it is in 1 device.

Please explain one device. Like a Split-circuit receptacle?

Yes split circuit on one device means two circuits on one receptacle. Only then will a 2 pole breaker be needed, both for residential and commercial.