For some reason, I can't use Negative Energy Ray to spontaniously cast cure or inflict spells. Is this supposed to work like that?

Spontaneous casting doesn't work with domain spells in NWN. Not sure if that's intended.

I think it is. Infact I don't think your even supposed to be able to prepare more than one domain spell even though in nwn you can.

If a domain spell is not on the cleric spell list, a cleric can prepare it only in his domain spell slot.

Yeah. Dem clerics be good!

Also, you can't trade domain spells for others, anyway, according to rules.

The cleric can "lose" any prepared spell that is not a domain spell in order to cast any cure spell of the same spell level or lower

Yep thats one of the cludge implementations thats carried over from BG games. Instead of limiting that slot to particular spell lists like it should (specialist wizards included) you just get an extra one to put anything you like in it. In fact the only reason a level 1 cleric is getting 3 slots is because they get one for their level, one for having 12+ wisdom and one domain slot.

In PnP as clerics the only thing you're allowed to put in domain spell slots is a spell chosen from domain #1 or domain #2 (theres 9 spells one for each level in each domain, 18 spells total). You're also allowed to put metamagic domain spells in there .. (like putting an 'extend'ed level 1 domain spell in a level 2 domain slot)

It's one of the fixes that even NWN2 has specified that they wont be fixing. A larger reason for the non-implementation of that problem (for specialists wizards)is they NEED to have a spell of EACH level of the sphere they specialise in so they can put something in that slot, this involves having 9 evocations, 9 conjurations, 9 illusions etc (for level's 1-9) so thats 72 spells minimum, so it's a lot of work.

Given that cleric domains can include ANY spell it's quite easy to put a spell (even if it's just a extra hold person at level 2) for each of the levels of a domain. Even if the official spell for that domain isnt implemented in the game you can simply choose a temporary replacement.

But heres hoping that it may be tackled down the track.

This is the way that it works in NWN, and although it may not be the best system, it's integrated very deeply into NWN and isn't really something that's viable to change. Here's to hoping that it gets better the next time they redesign the engine!