Don't you think that the main story in BG2 sucks?
In the beginning, it seems that Jon wants to unleash your "high potential". He tries to seduce you in your dreams. But it later turns out that you don't improve at all after his treatment. The story changes! (Don't tell me it was a scheme of Jon) Something's wrong here.
Also, the mysterious romance with Elesine amounts to nearly nothing.
In short, the story begins well but ends badly.

I don't like what you learn of dear Imoen either.
It's like in Star Wars: the girl who could be a fiance is turned into a hidden sister!

I don't think the story sucks at all -- Irenicus, like so many other villains, is full of $&*!. He tempts you, sure, but he never plans on delivering. He just wants you to come willingly. Though I'll admit, a better job could have been done in some respects.
I don't see the fact that a deity for a father is shared makes you romantically incompatible -- there's a mod out there letting you romance Imoen, and as has been discussed on other threads, it's not that weird.

Except for that you guys grew up together.

It would also be weird for a brother to be romantically involved with his adopted sister, wouldn't it? So you could say that they don't have the exact same parents, but I think they did grow up as brother and sister (or am I seriously wrong now?)

Anyway, I like the storyline. Maybe it's because I only played good so far. Maybe if I'd been evil and would've wanted the power Irenicus promised, I would be upset. But nothing's wrong with that. If that happens, it's just stupid to trust such a villain.

Imoen and the Main Char are brought up as buddies and never told their true heritage. only Jon lets them know. Imoen and the MC have the same father.