Notion sucks in PDFs, Apple Note is ugly and doesn't have Markdown – what else?

Notion is such a weird product. I like 80% of it, but the other 20%... The biggest issue is how bad it is with PDFs. It doesn't even search them, and there are no annotations. Apple Notes is just miles ahead - while way too simple elsewhere (no markdown, ugly typography).

My work involves writing a lot of notes, and then working with a bunch of PDFs (mostly papers) and web pages / articles. Currently, I collect everything in Apple Notes - I embed PDFs, and copy text versions of the web articles into notes as well. To get text versions of articles, I use Bear web clipper - it turns pages into pretty nice markdown notes.

Now, on one side, Apple Notes is great in combining all these different types of data. It also syncs well across all of my devices, and as it is pretty simple, to use it is generally pretty convenient. Its search is the best I've seen - searches through text, PDFs, images, and search is generally very fast.

However, I have 3 main issues with Apple notes:

1. no paragraph spacing - any long text is just ugly and hard to read. This is especially relevant for web clipped articles.... The workaround I am using right now is generally turning them to PDFs before I add them to notes.

2. No good AI support. Apple Intelligence is a joke. Notion has great AI, and I enjoy using it in our work Notion instance - I would've loved to have something like that.

3. No version control, and no version history. Once again, Notion has a great version history that gives certain peace of mind when dealing with a lot of notes, at least I always know there is some backup. I have my Time Machine backups for Apple notes, but it is not the same.

Generally, Notion is a very nice product, and it would've been perfect if not for its PDF handling... No search within PDFs, and no annotation capabilities just make it unusable for me, which is a great shame.

At the same time, I am wondering if there is a software that solves all my problems, I am just not aware of it yet. Is there something better that you would recommend?