The technical differences are large when compared to the technical similarities.
CTSS was built for a modified IBM 7094 system while ITS was built for the DEC PDP-6 (later PDP-10). Both of these machines were organized around 36 bit words, but the similarity tails off after that. Both machines lacked a hardware page map, and did not attempt to provide virtual memory capabilities to the timeshared applications. But they both had hardware and software features to protect the system and the users from rogue programs. Later on, DEC PDP-10s were modified to provide a third party page map, and DEC came out with a processor, the KI 10, that had a page map.
CTSS was intended to make timeshared access available across a wide swath of the MIT campus, and to a varied user community. Terminals were set up a long ways from the data center itself. These terminals included the golf-ball print head and the keyboard from the IBM Selectric, with communication gear built in for connection to the computer. Best keyboard I ever used.
ITS was intended to organize usage of the AI PDP-6. There was almost no security at all. They preferred to depend on security through obscurity. If you could figure out how to use the machine, then you probably belonged in the user community, regardless of your formal status. But remote access was initially not supported at all.
The "Incompatible" in ITS was a humorous reference to the "Compatible" in CTSS. For comparison purposes, the name unix was chosen as a deliberate ironic reference to the "multi" in Multics.
While the people who built ITS would have called themselves "hackers", this can be misleading in today's context. They were information anarchists, but they were largely benign, at least in their intent. They were also somewhat project leadership anarchists. Very little top down management went into ITS, as far as I could tell. Instead, people built things, and persuaded other people to accept them based on the usefulness of what had been built. Nonetheless, ITS exhibited a uniformity of design that makes the products of more formal development efforts look like a hodgepodge. The hackers respected each other.
The user interface for ITS was the debugger, DDT. The user interface for CTSS was a very early prototype for interactive user command languages that came along later. Examples of such later command languages might be the command language for TOPS-10, a timeshared operating system from DEC, or even the command shell for MS-DOS.
The primary language for ITS was LISP (apart from assembler). One of the widely used languages on CTSS was Basic, adapted from Dartmouth Basic. This reflects the different nature of the user communities for the two systems.
Most of the above is from personal recollection. I used both systems, about fifty years ago. I apologize for the lack of specific pointers to more formal history of the two systems. Here are a few links to get you started.
List of ITS machines
Writeup on Prof. Corbato architect of CTSS
Hackers: Heroes of the Computer Revolution.