Ed has to keep telling Officer Rhodes how to do his job or take command from him throughout the film makes sense later on when it's revealed that Rhodes is really an escaped prisoner disguised as a policeman. Rhodes also being creepy and staring inappropriately at Paris are also hints.
During the scene where the multiple personality plot was uncovered, the judge is thumbing through Malcolm Rivers' diary. Every couple of pages features a dramatic shift in penmanship, illustrating Rivers' shifting alter egos. The last we see are the words "Timothy/Timmy York" written over and over in red, large block letters for two straight pages. Hint, hint.
Ed and Caroline were traveling between Las Vegas and Los Angeles, Paris was traveling from Las Vegas to Florida, while Rhodes and Maine were traveling to Carson City from Las Vegas. It makes zero logical sense for them to end up in the same motel, as the routes (from Las Vegas) go south, east, and west respectively. As the motel was in the mind and not on the highway, it doesn't have to make sense.
In the very beginning of the movie, Malcolm Rivers insists that he made up the "I saw a man who wasn't there" poem, whereas in fact it's the first stanza of the 1899 "Antigonish" poem by William Hughes Mearns. This foreshadows the fact that Rivers would appropriate the aspects of the external world into his own Mental World - and that some of the people we see "are not there" indeed.
In the end, no character in the movie had a Trauma Conga Line quite like Paris - topped by the ending of course. And this is perfectly logical because she represents the person Malcom Rivers hated more than anyone else - his mother.
The killer being Timmy York, the child makes sense. Malcom River's mind fractured when he was 8, roughly the age Timmy is. It is the strongest manifestation of Timmy's psychosis as Timmy was closer to Malcom as he originally was before he went insane than any other personality.
