The CP-e pump is essentially an upgraded stock pump, but like stated above there is some more to it than that. For instance, they break in the pumps with the new goods by pressure testing them prior to sending them to you. Each pump comes with a certificate or a log or whatever of the test results to verify that your pump is working flawlessly and gives you no problems. CP-e's pump also comes with a lifetime warranty, whereas just installing internals does not.
And as far as I know (don't hold this to me) the CP-e pump WILL work with the gen2's, because it's the same MZR 2.3 DISI that the gen1's have.
As far as I'm concerned this would have been a great deal for anyone not looking to spend upwards of ~$700 on a new CP-e pump, but the peace of mind the lifetime warranty with the CP-e pump is enough to have me waiting until they're in stock near hear for me to get one instead of just internals.
Not to mention DIY'ers installing the internals must be very careful and very precise... you never know if you're installing a shim off slightly or if you reinstall the retainer button wrong, etc. and that can cause serious issues compared to having a brand new lifetime warrantied professionally installed pump at the ready.