Hickory: It's the Unity engine not the programming or the game itself. The files are on par with saves from Pillars of Eternity 1 & 2. The Unity engine is also the reason for slow load times.
cafeine_: They're using a custom save system, different from the one in PoE. (you can check it out yourself, Pathfinder's format is a bunch of json files and PNG images stored in a zip file, can't remember PoE's format off the top of my head but I'm sure it's done differently). What's happening with these games (and it's been happening for a long time, check your Fallout 1 saves and I bet they're the same), as other people have said, is as you visit locations their state changes and it's recorded in the save file. There are different ways to do it, but when you're designing a game on a short budget I guess once you have a system good enough you don't necessarily have the manpower/budget to tweak it so it eats less disk space/bandwidth.
That said yes Unity games can have slow loading times, there are solutions for this but it's also a manpower/budget problem.
Edit: forgot to add, early saves are much smaller, my first save (right at the beginning) is 664kb.
As mentioned above, the reason saves are ever-increasing in size is that *everything* is saved.
There is a log file in the save that starts with your character creation and is never deleted or rotated.
Every area you load has every single piece of information pertaining to it saved in the save file. The full list of the mobs you fought is part of that, including their locations, and their full list of attributes. Each mob requires a few kB: multiply by the thousands of mobs you slay through the course of the game, and you get several MB.
Each and every piece of loot you *ever touched* is also saved in the file as part of the area it's in, as well as logged (in the global log file, which dertails when and where you acquired it, each time you moved it to a container, and each time you dropped it or sold it), and possibly included in the player file as part of an ever-growing array of data (since the player file also seems to be rather larger than one would expect).
Part of this is of course necessary, other parts are not strictly necessary but are still a good idea, but others are a bit of a head-scratcher. Specifically, there is no nead for a completely, utterly dead mob to retain its full information; keeping a log is a great idea for debugging, and I'm sure it allowed the devs to fix some problems in hours instead of weeks, but this log contains loads and loads of text: it's very easy for it to become the single largest file in your save zip. Text does compress rather well, but there is a limit.
Another fun fact: *each time you load a save it gets modified*. Yes, really. There is acounter of the times you loaded the save, which of course needs to be increased each tim you load the save, in order to work. This means that you will always reupload the last save you opened. It also means that a critical error during this portion of the loading process, which seems entirely unnecessary, can leave your save file corrupted.
And of course, with saves that are several megabytes in size, or even tens or hundreds of megabytes, reuploading a cloud save because you loaded it once is a waste of bandwidth.
The save system isn't the largest issue with the game by a long shot but it could have been better implemented. It still can, for that matter.
