Over the years, I have made a set of personal balance tweaks that are much narrower in scope than large overhauls such as BTBGI. I wanted a "mostly vanilla" experience and good compatibility with other mods. Also, I noted that GCD prefers Fortify Maximum Magicka to Fortify Magicka, but does not come with a patch for all the vanilla items with Fortify Magicka.

WGI is a classic, but it is old - it doesn't cover Tribunal and Bloodmoon, it doesn't incorporate MPP fixes for magic effect sounds and names, and it is not GCD-friendly (OK, it's only a minor conflict).
BTBGI is too drastic for my tastes. It removes a lot and changes gameplay a lot.
Srikandi's alchemy adds many new ingredients, but also changes vanilla alchemy a lot. It removes Fortify Intelligence but keeps Fortify Luck, which has similar exponential stacking.
hollaajith has made an Armor Overhaul and a Weapons Overhaul. I love both, they're up-to-date and provide a more consistent and balanced vanilla experience, but the GMST changes that change the type (Light/Medium/Heavy) of a boatload of mod-added armors broke my heart. When I get around to playing Morrowind again, I'll only use the Weapons Overhaul.

Here's a description of some of the modules:

Enchantment GMSTs:
Easier to create enchanted items yourself (6x for Constant Effect, 3x for others)
Cheaper to buy enchanting (0.5x)
Cheaper scroll enchanting (0.1x, MCP dependent)
Slower charge regen (0.8x)

Alchemy (ingredients and potions):
Fortify Magicka -> Fortify Max Magicka (GCD friendly)
Fortify Intelligence -> Fortify Willpower (avoid exponential stacking)
Fortify Luck -> Fortify Agility (avoid exponential stacking)
Lightning Shield -> Resist Shock (might remove this; it was because Magical Trinkets of Tamriel uses this magic effect)
Cheaper player-made potions (harder version reduces price to 0)
MPP potion naming merged
Restore Attribute potions 2s duration (GCD friendly; GCD's own patch uses 1s duration)

Magic Effects, Spells and Enchantments:
WGI v9 Magic Effects, Spells and Items (Enchantments mostly)
MPP fixes merged (spell sound effects and names, enchantments)
Resist Paralysis 2.00 -> 1.00
Fortify Magicka -> Fortify Max Magicka (GCD friendly)
Fortify Max Magicka 4.00 -> 10.00
Restore Attribute/Skill at least 2s duration (GCD friendly)
Spellmaking/enchanting restrictions (Chameleon, Fortify Skill/Attribute, Charm)
Chameleon item nerf (robe_elanande_en, am_amuletofshadows_en)
Some Shield enchantments replaced with other defensive magic effects (for looks; only Ebony Mail and Wraithguard so far)
Hortator items Constant Effect

Daedra:
CE Bound Weapons (and sometimes Bound Shield) for Dremoras and Golden Saints
CE Shield for most Dremoras so they don't waste time casting spells. Also they should have high AR with all that daedric armor.
Dremora Lords may drop daedric armor and weapons (5% chance)
Winged Twilights can fly
Winged Twilights drop deadra hearts
Summoned daedra get non-AoE (Area of Effect) versions of their spells
MPP fixes merged (corpses persist, soundgen)

Armor:
Daedric, Ebony, Her Hands (except shield): 1/5 value
Glass: 1/4 value
Indoril (except shield): 1/2 value
WGI ebony and daedric tower shield stat tweaks
MPP fixes merged
Better Morrowind Armor, Complete Armor Joints and Snow Prince Armor Redux merged (with some cleaning and bugfixing)

Leveled Creatures:
Un-levels all Vvardenfell leveled creature lists.

I like most of these changes.