Usability wise, not much. Ive used both 1st and 2nd gen pencils, currently on 2nd gen.
The only drawback that I see is pairing and charging 1st gen pencil. Now, imagine, they upgrade basic iPads charging/data port from Lightning to USB-C, yet keep the 1st gen pencil which can be paired and charged only by plugging it into iPad(OK, you can charge it straight from charger as well, but you get the point) and to do so you need additional ADAPTER for it to work which you have to PAY for extra.
So, its easy to lose 1st gen pencils cap, its also easy to lose charging/pairing adapter. When you buy 1st gen pencil you get one extra tip and also lightning-to-lightning(M/F) adapter for direct charging with charger, again, another piece of equipment to lose.
Not cool, IMHO.
As mentioned above, they probably cheaped out on clearing 1st gen pencil stocks/or sort of and also cheaped out on redesigning wireless charging location on an iPad to one of its sides, because its their "cheap" iPad and not a Pro model.