Same problem here. Load times have crept up to 30 seconds and keep going up. This is running off a Samsung 840 EVO SSD with a Quad core i7 with 24GB RAM.
The save game files (I think the main save files are in %USERPROFILE%\Saved Games\Pillars of Eternity) have increased from 160KB to 2MB in three days of play.
The temp save files (%USERPROFILE%\AppData\Local\Temp\Obsidian Entertainment\Pillars of Eternity\TempSaveData) are between 100KB and 1MB for the .lvl files with no show of increase over time. MobileObjects.save is 2MB.
Looking at Resource Monitor, it seems that during load times there is no bottleneck in disk or network throughput as you'd erxpect, but one CPU core spins up to maximum usage indicating that the load operation is single threaded and CPU constrained. I suspect that as the save file builds up game state it's taking longer to save/load this file due to the amount of clutter it's having to serialize/deserialize.
Hopefully this can be optimised, otherwise it would be great to be able to switch off autosaves on screen transiitions which I suspect are taking up most of the extra load times.
Hope this helps and thanks for such a great game!