YMMV, but I’ve always used Goodreader from the days of DTTG1, and it still offers a very feature rich and solid option. It’s still my go-to in terms of annotating PDFs.
Its key-feature for my (very specific) usage scenario in annotating, is that it is one of only a handful of apps that ‘stores’ my most recently used highlight-colours. I use several specific colours repeatedly when I annotate PDFs, both on the Mac and iOS. Its ability to ‘remember’ these colours, and have them available from the quick-menu (given how regularly I rotate through these colours whilst annotating) is a huge plus-point for me - but then, I’m probably an outlier in this regard…
I use Notability for just about everything else involving the Pencil.
It allows for synchronous audio recording, which is “paired” with the writing inside the document. In other words, the text is greyed out initially whilst using the audio scrubber (of what was recorded), and is the ‘revealed’ as you get to that part of the writing that coincides with the audio - and therefore allows you to quickly get to the audio component surrounding a piece of writing, and is very useful in the context of meetings and consultations.
It also has a Mac app, which syncs via iCloud - and does so without issues - which is its key feature for me, as I am able to generate secondary reports from my Notability meeting ‘recordings’ on my Mac only, should I wish to - and serves as a useful backup.
It’s not a feature-rich as Notes Plus, which is another good Apple Pencil focused app I downloaded after seeing many recommendations for it. That said, it is very feature-rich, and I’ve not really taken to it, since Notability and Goodreader more than adequately covers my needs. Still, many swear by it, so might be worth a look.
Lastly, I’ve dabbled with Liquid Text, and still need to spend more time with MarginNote. The former offers some very nice (and fairly unique) features with regards to viewing and interacting with PDFs, but lacks some of my required features outlined above.
MarginNote looks to be the most interesting of what I still intend on sinking my teeth into. It’s quite a complex beast - but assuming you get to grips with it, offers some of the features of Liquid Text, but is a combination of PDF annotator, outline and mindmap app - coupled with a text summariser and flashcard creator - all rolled into one!
So assuming you can get it to do all it promises, could be a real powerhouse.
That said, as alluded to earlier, whether these amount to the ‘best’ companion app for DTTG2, really depends on what your specific needs are. But I would hazard a guess that you will find what you need between the suggestions that will/have already been made in this thread! Good luck!