Previous TES games had only Daedra and undead summonable, but the ghostly wolf conjured by the Summon Familiar is neither Daedra or undead, unless I miss a bit of information where it is said to be a ghost of a wolf. If it is the ghost of a wolf, why is it the only etheral undead summonable in this game (other than a few special effects I shall not spoil)? If it is not undead or from the planes of Oblivion, where does it come from? Is it ever explained?

How does Clairvoyance work in terms of lore? Why is it an Illusion spell if it's not manipulating someone's mind? Are you manipulating your own mind into showing the path to a place that you shouldn't really know the path to (except if a quest giver gives directions)? Is it ever explained?

It's not the ghost of a wolf, it's a companion spirit. Lore-wise, it probably fits in with how witches in other games have wolves and other animals in their lairs, as servants.

Clairvoyance can probably be explained as manipulating yourself into seeing a clear path towards your target.

The familiar is probably more like an ancestor power, the Dunmer summon ancestors I just imagine the wolf is a dead pet, or something like that.

On that note, why are invisibility and muffle under illusion?

You cast invisibility on yourself and your body becomes invisible, same concept with muffle. That isn't a 'manipulation of the mind' it's more suited to alteration IMO, a 'physical manipulation of the real world'.

If you cast invisibility on an enemy, then you were invisible to that enemy then illusion is fitting, but I think alteration is much better suited.

An illusion is a distortion of the senses. Invisibility distorts the senses of others to make them think your invisible or makes them not hear you. Undead and Daedra are immune to invisibility unless you have master of the mind. Its not manipulating the physical world at all. Alteration is about the reality of change, Illusion is about the appearance of change.

In Morrowind you could summon Centurion Sphere's by reading Secrets of Dwemer Animunculi and http://www.uesp.net/wiki/Tribunal:Unique_Items#Barilzar.27s_Mazed_Band, let you summon fabricants. The spells to summon wolf and bear could also be acquired from the bloodmoon expansion. Bears was also a possible summon in Oblvion with the spell tomes DLC

Oh yeah, I forgot about those Morrowind spells... But how do they work too? Maybe magic isn't as consistant as I thought.

Wrong, invisibility works on undead without the master of the mind perk, it becomes more effective as you take perks such as animage.

It would be entirely plausible if you casted it on an enemy and you were invisible to them, but you become invisible.

If I cast invisibility on myself, then run half a mile to a different location, I am still invisible to them. Are you suggesting you have some sort of aura around you manipulating the minds of every near person? To me it looks like the spell that manipulates the light around you, resulting in an invisible effect, so it's a 'physical manipulation of the real world'.

If the spell manipulated light around you to make you invisible or passed through you. Then you wouldn't be able to see as your sense of sight is based on light. You say its a physical manipulation of the world however the creators of the game disagree with you. The fact it becomes more effective when you take perks such as animage and is broken when you perform certain actions is proof that it is an illusion.

lets see, there is a realm in oblivion called the "soul carin" (this is from the UESP) that is inhabited by the dead and the "perfect masters," so the dead come from there, supposedly, including the wolf spirit you can summon. clairvoyance has no explenation lore-wise and is only there for a game mechanic i think (sorta like how crossbows are in skyrim lore-wise but they are excluded in the actual game)