In terms of quality, it's pretty much the consensus that the SE line is, and always has been, on par with the best quality guitar you can get in the given price range. I don't know if "quality" has been improved, per-se, but many would probably say that the "design" has been improved. However, there are probably plenty of people who prefer the traditional design.
In terms of changes, a few things I can think of...
Your 2009 should have a flap top, like cshallcross mentioned, and the newer ones have a beveled top. Pickups have definitely changed, along with coil splitting via a push-pull tone pot. Also, the 2009 should have the traditional volume/tone/3-way toggle setup. The newer Custom 24's all have opted for a blade switch on the lower bout of the body.
New in 2017 was the newer headstock logo that more closely resembles the signature seen on the core (US) models.
Also, I believe manufacturing has been moved from Korea to Indonesia (which I believe is really of no consequence, but a change nonetheless).
I'm sure there are more changes that people will chime in with...