My 2nd generation apple pen won’t connect to my 6th generation iPad

Correct.

The second generation Apple Pencil is not supported by the sixth generation iPad. iPad6 can only be used with a first generation Apple Pencil.

Here is Apple’s definitive compatibility list for Apple Pencil and iPad:

Apple Pencil compatibility - Apple Support

The first and second generation Pencil use an entirely different pairing and charging interface. 

The second generation Pencil can only be used with iPad models that have the magnetic/inductive dock that is exclusively designed for the Pencil. Charging is controlled via the iPad magnetic dock.

The first generation Apple Pencil uses the physical Lightning port of the Pencil and host iPad for both pairing and charging the first generation Pencil. The first generation Pencil can also be charged using an inline charging adapter and the iPad’s Power Adapter. This pencil can only be used with compatible iPad models that have a Lightning connector; with the sole exception of the new iPad10, requiring a special adapter, iPad models that feature a USB-C port lack any means by which to pair with a first generation Pencil.

In summary, the Apple Pencil models are not interchangeable - and can only be used with the iPad that has appropriate internal hardware.

Have you held/left it on the magnetic charger for a few moments?

With mine, when I got a new iPad, I put it on and it said connected and then I took it off straight away and it didn't work.

But if I left it on for a couple of seconds (until it showed the battery level) it meant it was then properly connected and worked fine.

Other than that, just a quick check if your Bluetooth is turned on on your new iPad too.

Regards,