I've been a lurker for some time in this forum, but I've decided to make an appearance in defence of the female cast (that is not to say that they have been underappreciated or such).
My top choice would have to be Loren and Elenor. I do find myself wishing that they have more (and more explicit at that) interactions with each other (might be rectified in the upcoming 0.93? hint, hint), but I simply adore the awkwardness that underlies their relationship. The love triangle scene at the end of Chapter 3 was particularly poignant: it gave us all a hint into how deep Loren must truly feel for Elenor despite it all.
For some of the above reasons, I would submit Karen and Elenor as my second choice. It is a bit dodgy to have her open to a new relationship immediately after losing her lover, but the appeal of a damaged, mature woman was just too much for me (and I'm sure, everyone else) to resist!
For a heterosexual pairing, I would have to pick Saren and Myrth. This came as a bit of a surprise to me. Being gay myself, I tend to choose exclusively gay storylines due to the dire scarcity of them in the first place. I tried out playing as Saren for kicks, blundered into romancing Myrth and was wonderfully surprised at the tastefulness with which their story has been handled. The romance was not at all in my face; it was as understated and evocative as Elenor's with Karen or Loren.
I similarly enjoyed Saren's romance plot with Draco, but I was especially irked by the storylines with Amukiki. I don't know why exactly, but my eyebrow twitched uncontrollably in vexation every single time a romance option with Amukiki popped up. I expected myself to dislike Rei, but the further I got in the game, the more he redeemed and endeared himself to me.
In conclusion, I adore all the characters (except for Amukiki, I'm truly sorry, but I just can't) to varying degrees, but if I have to choose my OTPs for this game, it'd have to be: ElenorxLoren and SarenxMyrth.