These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
YMMV: RE: Alistair
Fan-Preferred Couple: Shiro seems to be the most popular character. The bonus scene acknowledges this, with the characters thinking up reasons as to why the fans liked him the most.
Fridge Brilliance: Shiro warning Merui about Travis, and then telling Derek to stay away from her. To the first-time player this may just seem like Shiro's being overprotective or acting on jealousy. However, upon The Reveal that Shiro is FionaWings, the player realizes that he just knew that it had to be one of them who was Alistair.
When you go through Shiro's room you happen to find out he was planning on purchasing a specific blade only usable by Knight characters like Merui's. When it is revealed that Shiro's player character is FionaWings, an Angel, it can hit you that this was an early hint that Shiro was really FionaWings! He was buying Merui that sword!
After meeting Derek at the mall, he emails you and says "I enjoyed today. Your a lot of fun to be with." There's someone else that replaces "You're" with "Your", namely Alistair.
Fridge Logic: Merui confirms that Travis, Derek, and Shiro were all online during lunch when the network went down, which is how she concludes that one of them must be Alistair. Travis was in the computer lab at the time, but Derek and Shiro weren't, and judging by various bits of Travis's dialogue the school doesn't seem to have be more than one computer lab... so where were the other two logged in from?
personal computers more than likely. Shiro is pretty wealthy, so it isnt to much of a stretch to think he might have been able to afford a laptop to take to school, and Derek could have his own laptop as well. There is even a throwaway mention at one point of the school having Wifi (which is probably meant to explain how they were on when not in the lab with Merui)