Most VPN clients distinguish between IPSec and "Cisco IPSec." For example, (Apple's) iOS treats them as essentially separate things.
But I can't find any explanation of what the protocol-level differences are. They may be minor, but there definitely appear to be differences.
Can someone shed light on this? Even just a pointer to a detailed explanation would help a great deal. Thanks!
From my understanding, "Cisco IPSec" is just marketing speak for IPSec with some pre-defined settings for AH/ESP, tunnel/transport mode, etc. pp.
When you read the RFCs, you see that they deliberately leave room for implementations...you, as the network admin setting up the IPSec connection have quite a lot of options to choose from for the protocol (and you need to). Cisco simplified this a great deal by saying "Both participiants do ESP, they have encryption modes X, Y, Z at their disposal, (...)".
I understand from your comment that you are wondering the differences between L2TP+IPSec and IPSec only.
When IPSec is used "alone", it can oper in two modes :
Tunnel mode is mostly used to connect two networks, from router to router, while transport mode will be used for road-warriors, devices (laptop, iPhone), connecting to corporate network.
L2TP over IPSec is similar to transport mode, connecting a remote device to a concentrator. The remote device can be however a router.