The Not-So-Good
Target number scaling very gamey. E.g. mammoth has better reflex save than goblin. Doesn't make sense in the world, but makes sense in a video game scaling world sense. There are monsters with AC 40, with attacks that roll +30 to hit. No plucky, clever plan by low level parties will ever succeed in killing a mammoth. It is like a video game, an MMO, where if you stumble into a high level zone you will be totally outclassed by unkillable animals.
Complex character creation. It is highly versatile. There are many character concepts, but lots to read. The core game has 12 character classes described over 166 pages. Creating "builds" is a big part of player fun and system mastery. The process is simplified by using digital tools like the PathBuilder phone app, but it's not simple.
Adventure paths are pretty railroady and combat focused. That's fine, I guess. To be expected. I would prefer more support for sandbox play, but I guess they know their main audience doesn't know how to play those. I created my own homebrew campaign, using a sandbox and the game system worked just fine!
Lots of conditions and plusses and minuses. Lots of overhead for players to manage. Thankfully Foundry does an amazing job, but I would hate to play this game with pen and paper. In Foundry you can just drag and drop the condition onto your token and it works everything out. With this complexity, your players need to be happy with reading and researching between sessions. If your players are more casual they may find the complexity a turn off.
Tons of options for ancestries and classes, incredible customization possible. Possibly overwhelming. Every time Paizo publish a book, they add new classes, feats, spells and magic items. Each of these is added to the Nethys website and also to Foundry. This is a growing mess of content that is overwhelming for new players and GMs. There are currently more than 3600 feats in the Nethys database. Let that sink in. This bloat is a barrier to entry for new GMs.
Complex to homebrew. I wanted to run a campaign set in the world of Dark Sun. I knew I would need to create a few items like homebrew ancestries, classes, etc in Foundry. Not a big deal, I thought. I was wrong. I was not ready for what a pain in the ass this was. The system is so detailed, that for each armour item I need to capture five or more data points. To create a new ancestry means creating multiple heritage items, setting up JSON lists of feats and abilities. If you want to play Pathfinder on Foundry, you are pretty much locked into playing in a setting that uses the default options. This cramps my style.
Kitchen Sink Fantasy. I do not like the Glorantha setting. It is just like Forgotten Realms where there are dozens of playable ancestries, and a mish mash of genres stuffed together. It has the fantasy wild west, with guns and explosives. It has swashbuckling pirate land. It has martial arts monks in fantasy Africa. It has fey lands with unicorns and leprechauns. It has no clear vision or theme. These options are built into the core game, are seen in spells and class abilities. If you want a narrow focus in your setting, with a theme, you will need to analyse the 160 pages of the classes chapter and excise player options. (Players hate it when GMs do that). And remember that there are multiple splat books that add additional options for ancestries and classes too.
Community has unfun people. I advertised my new campaign on the Pathfinder Discord LFG group. I had 13 applicants in the first 15 minutes. So there is a lot of demand for GMs. Many of these players are dedicated to building the most optimal build by multiclassing and beating the game system. Some players got grumpy when I tried to restrict the game to the Core book only. One player was incredulous that I would dare to try GM the Perfect Game without first having read thousands of pages of splat books. Some players consider certain optional variant rules as The One True Way to play (because it enables their theory crafting character building). A game this complex demands dedication from players, and some people view their system mastery with pride, and want to play the game in a way I don't enjoy.
Magic Items fun is fenced off. I am accustomed to the OSR style of magic items, which encourage players to have loads of fun with goofy magical gadgets that allow PCs to surprise me and create crazy scenes. "Oh remember the time we reversed gravity on that pool of acid!" But Pathfinder is so fixated on "balance" that a lot of the fun has been stripped away from magic items. The fun ones are all rated level 15+. The lower level ones have exciting names, but underwhelming effects. Like the "Mistform Elixir" (level 4) which sounds like it turns you into a mist. Nope, it grants the Obscured condition (5 in 20 miss chance) for 3 rounds. Many wondrously named items are kinda lame, and merely give +1 to some ability temporarily. Maybe I grew accustomed to the hijinks of the Cypher System in my last campaign?