Personally, I've used FM transmitters (a couple brands no less), 3.5mm jack, USB and Bluetooth for transmission to my car within the last 4/5 years (jeez, was it really 2007 when the iPhone came out?!).
FM isn't unreliable, or I've never had that... but the bigger issue it faced was noise... sometimes it was really annoying and present, other times it was just soft static in the background from the low signal transmission. In an older mustang, there's a removable radio antenna that made a huge difference in clarity by removing...
3.5mm is great; sometimes its a little soft, but it's really pretty good otherwise.
Bluetooth is amazing. If you go the aftermarket route, just get one with bluetooth support... I don't think you'd ever regret it.
USB.... Well, its a love hate thing. I love being able to charge my phone + get slightly clearer audio than BT in my car, but it really bugs me that my car takes over the iPhone's music interface so I have to go through its menus to get at my music (not ideal, in my opinion...).
Anyway.. there's the little insight that I've got.