I think you're missing the complexity here, rei. Hiroki obviously considers Elise his most important person at the end but we never really get the sense that he's physically attracted to her.
npal's view pretty much matches mine and my recollection is that he was a big Elise supporter .... I've heard the manga does a better job of communicating the notion that Hiroki at least shows himself as being *physically attracted* to Elise whereas the anime treats the pair's relationship as almost purely "father-daughter-platonic" for the whole series til that end credit eyecatch. The last few episodes show the Kiri side of the triangle faltering (he seems to be just going through the motions as something he "ought to do") but the Elise side never really heats up in the physical domain to correspond even in a subtle way.
No one else is spoiler tagging so here goes...
Hiroki's motivations aren't that hard to understand ... Elise is important to him, he doesn't want to lose that bond. In the end, that simply is more important to him and we grieve for Kiri. But the bond with Elise has been portrayed as totally platonic from Hiroki's side throughout the series so the end eyecatch becomes a "wtf?" with no lead up. A few extra minutes of scenes scattered throughout the series or even an occasional blush from Hiroki would mitigate that.
Anime series are often very sketchy in storyline and viewers have to infer depth which often doesn't actually get portrayed but while the writers did a pretty good job on the Kiri story thread rise and fall ... they faltered just enough on the Elise side that even many Elise supporters didn't buy that last little snapshot in the blankets.
Overall, its still a pretty good ero-conversion anime and I wouldn't tell anyone NOT to watch it... the Hagino and Tomoko moments are worth it alone
EDIT: after some offline conversation with rooboy, I should clarify that my description of the Hiroki-Elise relationship for most of the series as "father-daughter-platonic" DOES not mean Hiroki raised Elise. She was raised by a relative and moved in with Hiroki to conserve expenses in expensive Japan to attend school where he taught. The anime implies that she's had a crush on him for a long time but there's not much in the way of explicit flashback. Hiroki, for 99% of the series, treats his relationship with Elise AS IF he were a caring father, not a possible consort.
I'll also point out that cousin-marriages are common throughout the world and legal in much of the US so any view deriding the choice on that basis has no basis in fact.
I'd love to see a spin-off series with Hagino and Tomoko going to college ... purely for literary reasons of course <snort, laugh>.