The freaky eyes kind of imply that it's Rider. It's probably one of her unstated abilities, and it might be the only way she can sustain her mana levels, not being able to obtain any from Shinji.
She's actually older than Shirou, she just calls him that out of affection for him. Shirou feels beholden to her, as he feels responsible for Kiritsugu's abandonment of her, and says that it's his duty as "Onii-chan" to protect her at all costs. Of course, near the end of HF, this dynamic is reversed, and it is Ilya who saves Shirou at the expense of her own life, not the other way round.
I feel that this is what makes HF the most complex narrative out of the three scenarios. HF is really principally about the sins of the father, his children, their siblings, and the ties that bind them all. Thematically it's rich and pretty dense, which gives it an epic scale that the other two never quite reach.
Play Again? Y/NRE: The sex-scene: It's implied that it's Rider using Shirou's dreams as a source of mana.
Maybe spoiler (not sure how far you've come)
Considering that both of her Matou Masters have issues (Shinji is jealous over Rin, Sakura of Rin) where that is concerned it's probably not unexpected of her to just assume that Shirou likes Rin.
"No, the Singularity will not happen. Computation is hard." -Happy EntWell, if nothing else, her Noble Phantasm kind of gives it away (if you know your mythology), although not in the obvious way.
Pegasus sprang from Medusa's blood, IIRC, after Perseus cuts her head off.
Play Again? Y/NIn Fate and UBW, Saber never really seemed all that powerful, as even though she was said to be the most powerful servant, she never managed to down another opponent easily. In HF though, Saber kills both Rider and Caster without breaking a sweat. Kind of refreshing to see the ownage.
edited 1st Dec '09 1:32:21 PM by neobowman
I finished watching the anime and got two questions...main difference between the anime and Fate Route (aside from the CGI DRAGON OUT OF NOWHERE thing, I mean)? and the second is: The Timeline where Shirou became Heroic Spirit Emiya...was similar to Fate route right?
edited 1st Dec '09 11:32:46 AM by vandro
I've said it once I'll say it again. Wicked I'm not keeping up with your liveblog because it's not Seorin's Let's Play.
And I thought that the anime timeline was the timeline where Shirou became Counter Guardian EMIYA.
Sorry, I can't hear you from my FLYING METAL BOX!

She's always been doing that, IIRC. It was blatantly obvious in the anime, which is why she was initially against Rin moving in with Shirou.