I've gone through all the Morrowind spells referenced in the UESP, put them in a big spreadsheet, and grabbed as many comparable Skyrim spells for reference as I can. I'll try to adjust our Skywind spells to match Skyrim's magic balance and upload my spreadsheet later, but for now I'll get the ball rolling on discussion with this thread.
Here are the notes/concerns I have so far. If it's not listed here, then it means I think implementation of that particular effect will be relatively straightforward.
Charm: Because Skyrim handles disposition so differently from Morrowind, this one's tricky to figure out on a design level. For now, I'm thinking of making Charm an all-or-nothing effect that temporarily turns the target into the caster's friend.
General School Changes: Spells like Light, Paralyze, and Turn Undead have changed schools between Morrowind and Skyrim. Do we want to keep the Morrowind versions of these spells in their old Morrowind school, or move them to their Skyrim equivalents?
Redundant Spell Effects: There are many spells in Morrowind that are redundant. For example, Rally Beast and Rally Creature are identical, though I think one is supposed to be a Touch spell. Greater Shockball is the same as a normal Shockball. My inclination is to adjust these spells so they're different, by: A) changing spell magnitude/range/etc when it seems the original developers made a mistake and B) converting the spell to use a Skyrim-exclusive effect when the spells are different as a matter of taste, e.g. turning it into a Concentrate spell (like Skyrim's Healing or Frostbite).
Sound: There's no spell failure in Skyrim. What do you guys think of having Sound act as a spell magnitude debuff? I.e., 30 pts of Sound reduces the target's spell effectiveness by 30%.
Bound Weapons: I'm inclined to use Morrowind versions of weapons even for Bound spells that exist in Skyrim, like Bound Battleaxe.
Summon Spells: Again, I think it would be neat to use the Morrowind versions of all these creatures.
Burden: This will be easy to implement, but I'm not sure if it will actually do anything. Oblivion had this problem: Burden had no effect on NPCs.
Levitate: No idea how to implement this yet, but I'm sure I'll find a way.
Open: Morrowind has no native Open Master Lock spell (though I think there is a scroll). We could leave this be, or convert one of the redundant open spells (Ondusi's Open Door is identical to Strong Open) to open Master Locks.
Shield: In terms of raw effectiveness, Morrowind's Shield spells far outstrip Skyrim's Flesh spells, even after all perks are applied. Personally, I don't have a problem with this--how do you guys feel about some Morrowind magic just being outright better than Skyrim magic?
Slowfall: Since you can't cast magic mid-air in Skyrim, 10 seconds seems an awfully short duration. I say we make Slowfall not actually slow you down, just remove fall damage. That way, 10 seconds is more than enough time to make the spell useful.
Drain/Fortify/Absorb Attributes: We could map these to skills/attributes (meh), or we could attach specific buffs/debuffs according to what the attribute did in Morrowind (so Strength would buff melee damage and carry weight, for instance). This is fine for drain/fortify, but...
Damage/Restore Attributes: This could potentially be mega-messy for damage and restore spell effects. My biggest concern is that Skyrim has no way to tell you if your Strength has been damaged, so you could be running around weaker without really realizing you need to restore strength.
Disintegrate Weapons/Armor: My best guess for what we can do is a disarm effect (that can effect armor, for Disentegrate Armor). Anything else isn't feasible in the current engine... (We can't affect a weapon/armor's improvement rating with scripts.)
Drain/Damage Fatigue: What do you guys think about adding a knockdown effect to this spell when the enemy has 0 stamina?
Mysticism: Here are my thoughts on what should go to what schools:
- Absorb: Destruction (Absorb Health is Destruction in Skyrim)
- Intervention: Either Conjuration or Restoration (with all the other "holy" spells)
- Detect X: Alteration, with Detect Life.
- Dispel: My best guesses are Restoration or Alteration?
- Mark/Recall: I think Conjuration is a good fit, based on lore in the Elder Scrolls novels.
- Reflect: I think Alteration fits here, too.
- Spell Absorption: Could be Alteration or Restoration (a la Wards).
Mark/Recall/Intervention: I think we should limit these spells to only work while you're in a Morrowind space, because they could really break things, especially when you add other mods to the list. With Skyrim, it will be very important for us to know if the player is in Morrowind or not, and this spell could break that.
Reflect: I see other mods have implemented reflect spells. I'll see how they do it. (For reference, Morrowind's Reflect is Reflect Spell. If only it was Reflect Damage, that would be trivial to implement...)
Cure Blight Disease: If we implement Blight Diseases as abilities instead of diseases, I can custom-script a spell that walks through all active effects and only removes abilities with the "BlightDisease" keyword. This will require SKSE, though.
Wild/Variable Spells: Spells that have a wide magnitude range as a selling point (for example, Wild Reflect, which is Reflect on self for 1-40 pts) present an interesting opportunity. I could probably implement a random spell range effect, but I think it would be more intriguing to combine these with some of Skyrim's built-in spell features. For instance, Wild Reflect could become a "cast on self concentrate" spell.
On-Cast Enchantments: Here are my thoughts on On-Cast Enchantments: Each on-cast enchanted item is associated with a specific spell. For instance, the Engraved Ring of Healing you find in the barrel at the census office comes with (for argument's sake) heal 3pts on self. When the ring is in your inventory, you get an "Engraved Ring of Healing" spell added to your powers. It's not associated with any school, and it has a set magicka cost. This power casts from your voice spell button so that you can cast with weapons out, and equipping the spell automatically equips the ring (unequipping the ring removes the spell).
Here's where things get interesting! You can disenchant the ring and put the spell on other rings. But why would you do that, if the spell's effects will always be heal 3pts on self, no matter how high your enchantment level? Because the enchantment comes bundled with a second effect: reduce on-cast enchantment costs by X%! So the more on-cast enchantments you're wearing, the cheaper it becomes to cast them, and you can cast them with your weapons out. The spells won't be as powerful as normal spells, but the added versatility makes up for it, I think.
Thoughts?

http://skyrim.nexusmods.com/m
http://skyrim.nexusmods.com/mods/9153
This might help you out a bit. Also, in Morrowind I rarely used magic, I was more of a melee fighter, so I'm not to sure what to say. =p
Mark/Recall/Intervention: I think we should limit these spells to only work while you're in a Morrowind space, because they could really break things, especially when you add other mods to the list. With Skyrim, it will be very important for us to know if the player is in Morrowind or not, and this spell could break that.
Good idea! I know some people will say something like "blah blah blah just use fast travel" but keep in mind, a lot of players who play our mod will probably wanna use as little fast travel as possible.