Lots of players are cheaper, faster, quieter, etc. And standalones in the PS3's price range are quite high-end these days, starting to get features like 4K upscaling and much better media playback features (MKV, FLAC, no arbitrary software restrictions on PAL video, etc).
The PS3 doesn't support all lossless audio formats for 3D movies, whereas pretty much any standalone does. Standalones have outputs like dual HDMI (for splitting audio and video when watching 3D) and analogue multichannel audio, which are both great for older receivers.
No infrared port on the PS3 is still a pain in the ass for anyone with a universal remote. I had to pay $55 for an IR to Bluetooth converter to use mine when the PS3 was my primary player.
You can get multiregion standalones, which is a big deal for someone like me who likes to buy movies from all over.
Updates? I don't think the Blu-ray spec is going to be updated again any time soon and I haven't seen major compatibility problems in years.