The primary difference I've found playing with the mods is that
1. Morrowind Crafting is more NOM (Necessities of Morrowind)
compatible. Crafting cooking does not conflict with NOM cooking. You
only eat NOM foods automatically, but Crafting foods can satiate NOM
hunger. If you play NOM, read the Crafting readme as you may want to
make a small chance to the NOM script to further improve
compatibility.
2. Complete Morrowind can be added in full or by type of crafting, if
you only want some of them. For example, you could load each
individual craft and leave out the cooking craft to be NOM
compatible. Also, you can choose to add on or not add on pieces that
change the landscape (e.g. cutting down trees for logs) even if you
choose the 'full' version.
3. Morrowind Crafting gives you more support in game and in the
readmes for "getting started" with the crafting. With Complete, you
spend more time wandering around wondering if anybody anywhere can
tell you more about "xxxx".
I like both mods a lot, and have difficulty choosing between them.
That choice, for each person, probably comes down to tiny nuances
between the games. For me, Complete doesn't muck with the basic
clchemy ingredients (beyong expanding them), which I like a lot, but
Crafting is more NOM compatible, and I miss NOM when I'm not playing
it.
The mods are available at Morrowind Summit / Planet Elderscrolls:
http://planetelderscrolls.gamespy.com/View.php?view=Mods.Detail&id=4077
http://planetelderscrolls.gamespy.com/View.php?view=Mods.Detail&id=443
(individual mods pieces also availble at this site)