In the Morrowind main quest, the player character turns out to be the reincarnate of Indoril Nerevar, who founded Great House Indoril. I was thinking, doesn't joining another great house in Morrowind sort of conflict with this fact? For instance, it doesn't make sense for the reincarnate of Indoril Nerevar to be the head of House Redoran, etc. Thoughts?

It makes perfect sense to me. Not all who lead are loyal, not all who are loyal follow.

It makes just about as much sense as him being a female Argonian The Nerevarine is not supposed to be an exact replica of Nerevar, just of his spirit (hell, one could argue its his archetype thats more important than the actual soul). In fact, a major part of the prophesies is about him being foreign.

Was he really founded it?

Yes, I am fairly sure Nerevar founded House Indoril.

That is correct. And why would the Nerevarine necessarily be in House Indoril? As an outlander, you weren't born into it, so you would need to choose to join it, it must be noted that at first, most people don't actually accept you as a Nerevarine, even once the fact that you claim to be the Nerevarine is known, the Temple says that you're a heretic, and even once the Temple changes that stance, not everyone necessarily believes you are Nerevar reborn, and at that point, the player may already have joined a seperate house. Just because the Nerevarine is reincarnated from someone who was in House Indoril long ago doesn't mean that he'll automatically be accepted into House Indoril.

It's not like the player is litterally Nerevar ressurected from the grave, I think people would be even more reluctant to see someone like that as their savior, seeing as you'd be a skeleton, if not a pile of ash or bonemeal. If a skeleton walked up to you and said "I'm an ancient hero reborn to save the land!" would you believe that? The Nerevarine is a new person who presumably has the soul of Nerevar, and his choices and actions won't necessarily reflect what Nerevar would have done.

So you don't think when the PC finds out that he/she is the reincarnate of Indoril Nerevar he/she would feel a bit guilty about being the head of a different house?

I think he would have the attitude that "we're all in this together" against Dagoth Ur and his minions. If the Nerevarine is Dunmer, there'd be even more solidarity than that.

depends on your PC. My Nerevarine thinks that the Indoril are a backward bunch too obsessed with the order of things to realize that Morrowind has moved past them.

As Hortator, you are belonging to all Houses. Indoril isn't even visibly involved - if at all, so it would be difficult to feel loyalty to them. Plus, you're an agent of the Emperor, you're not supposed to be emotionally involved...

My argonian embraced the Telvanni with open arms; nothing like a house full of wizards who believe might-makes-right. He also owned a lot of slaves. But don't worry, he's not picky on race. But, then again, he was more overjoyed with destroying the dunmer way of life by neutering their gods. Not that he was racist against the dunmer, but he's an agent of entropy, so anyone is fair game. It just so happened his target was pointed at Morrowind,

My nerevarine didn't give the indoril much thought. Out of sight out of mind.

My Nerevarine wears Indoril armor whenever he is going someplace public... don't ask where I got it :whistling:

Walter:
The Nerevarine is intentionally a http://tvtropes.org/pmwiki/pmwiki.php/Main/AFGNCAAP, a blank slate, so to speak, so Not having a canon Nerevarine avoids the whole debate about who he or she is because he or she could literally be anyone... thus the whole point of roleplaying games. Your Nerevarine was not my Nerevarine, who was not their Nerevarine, etc.

*this post may have been incredibly genre savvy

Completely true. However, just about every Open ended RPG is like this.