After reading a couple of other reviews I decided I should throw in my piece...
I watched Episodes 8 & 9 back-to-back since I was away on vacation for a bit. My girlfriend and I usually watch them together, but long story short, she had not seen 9, 8, 5, & 4. So, after I had seen the twist, I kept it a secret and decided I would willingly watch those episodes over again to have a look for hints.
In the restaurant, the waitress that Travis winds up sleeping with does NOT acknowledge that Gellar is even there at all. Good.
When the "whore" gets released by Travis, she tells the police that there were two of them. This is possible since she was blindfolded the whole time and it is quite possible that Travis speaks in Travis' voice, but speaks in Gellar's voice when he switches. Again, he is pretty screwed up.
In the scene where Dexter has the wire around Travis' neck, there is a small hole... After he tells him to get out and his car will be at the museum, Travis dials on his cell phone and has a conversation with Gellar. This bothers me a little bit since if he hits speed dial and we actually do hear the phone dialing, we should then hear either a voicemail, or an operator error message, or busy-signal, or whatever. I would have preferred if we did not hear the phone dialing, but this can be explained away (i.e. overlooked?) by saying perhaps the phone did receivea voicemail or a busy signal but the show didn't let US hear it - but in his mind he heard Gellar and proceeded to converse with him. After all, he IS pretty screwed up!!
Someone said that Dexter saw Gellar enter the university to kill professor Casey but in actual fact, Gellar appeared for a brief 2 seconds and it was Travis that saw him and said, "There's Gellar... Let's go," while Dexter actually has his eyes closed.
One thing I was a little bothered by was how quickly Travis rescued Dexter from the elevator shaft. Where was the body put so quickly? And how was he able to"prepare" the professor after being dropped off at the hotel room and set up the booby trap for the blood to fall, drain him of blood, etc. return to the hotel and write on his walls, etc. Then when we cut to the next day, it is sunrise. So it is amazingly fast progress for someone to do and then appear in his next scene clean as a whistle. Also there is no blood anywhere in the lecture room.
This and only this part made me frown... It would have been better if there was an extra day put in there to give this all time to happen. However, in the meantime, there isn't anywhere that says it was the immediate next day but it sure does seem like it.
I guess the reason why I didn't see the twist coming is pretty simple... I haven't been trying to read too much into this. I haven't been reading and chatting with other enthusiasts to get these notions into my head. Today is my first time ever logging onto this site to read anyone's "hypotheses" and I was kind of feeling like the season was being forced along for awhile until I let go of how great the previous seasons have been and decided to dumb myself down a bit and stop looking for the next big step... I had to watch it for what it was... a mini-series based on solving a serial killer with his clues being left behind. When I did that, the season is actually quite entertaining especially with the humor from the sideshows going on and the sub-plots it has within - probably put in there to prevent us from trying to think too hard all of the time.
But with a twist of this magnitude, and with the biggest achilles heel happening in the same episode as the twist, I do feel they should have put an extra day in there to give Travis time to set up the kill scene.