There's well known mod for Disciples II Dark Prophecy called D2 Nevendaar Rebalanced. Its author put up a solid work to fix/tweak some glaring issues in the base game (it's not compatible with Rise of the Elves), but stopped just after releasing it.
According to his mod description he has no issues on someone continuing his work, so I decided to make some changes to D2 Dark Prophecy myself on top of his tweaks.

Link to my mod:
https://www.moddb.com/mods/d2-nevendaar-rebalanced-20

Purpose of this tweaks is to make less used units more competitive, as I found out that with base mod I still didn't use many of them.

If you have any feedback, feel free to post it here or on moddb mod's page.
Please not that it's for the base game, not for the Rise of the Elves expansion. Also please note that those changes are made on top of D2 Nevendaar Rebalanced mod, so downloading base D2 Nevendaar Rebalanced is still necessary to get the "whole package". I'm gonna publish only the files I've changed.

Empire:
- completely changed Elementalist's class as summoners are absolutely useless in this game:
- got rid of his summoning elementals attack, instead he now has lower tier mage's aoe 30dmg attack with hermit's lower initiative (33% chance) -> both with air source, 40 initiative
- every level up he gets 5hp, 3 dmg, 1% hit chance for both attacks (those are mage's lvlup stats)
- changed his class description so it doesn't mention summoning creatures, but instead something appropriate to his new abilities

- added revive to Imperial Priest as matriarch already has secondary Cure on the same tier
- increased healing for Hierophant from 120 to 140 so it's double the amount of prophetess' healing
- changed Angel's attack source to air as it fits better than mind for 'holy' attacks (like holy bolt for example) and also fits empire theme, and isn't unblockable as life would be
- slightly increased Angel's hp from 225 to 230 to further emphasize the role of "hp tank" on his tier (10 more total hp than paladin, 20 more than grand inquisitor, yes i like round numbers)
- given death ward to Angel - it fits its lore, isn't OP like immunity would be, and makes him a bit more unique and useful for certain fights (like vs. undead)
- changed Paladin's hp 175->190 so its total with armor 10 more than grand inquisitor (same as it was on tier 2 and 3), especially that he has no wards/immunities
- changed Defender of the Faith hp 225->230

Mountain Clans:
- added druidess' Cure to Alchemist, increased his XP to next level 325->650 - no one used Alchemists when the other unit had a powerful buff AND cure
- added Lower Damage secondary attack to Flame Caster (33% chance to hit, fire source), lowered his initiative from 40 to 30
- increased Forge Guardian damage from 70 to 80
- increased Wolf Lord's hp 225->250 and aoe dmg 40->50 - he was too squishy for melee with his wolf form and with aoe his dmg was way lower than hermit's on the same tier
- added air wards to Tempest Giant and Elder One - their counterparts have water immunity so it seemed fitting to add at least wards to them too
- increased damage by 10 for both Tempest Giant and Elder One

Undead:
- changed Nosferat to hit only 1 target, but with standard scouting leader dmg (40) and hit chance (85%), initiative stays the same (50) - now he's like all other scouting leaders instead of being an abomination with weak 6 targets attack... we have mages for that and i always hated this "feature"
- changed Nosferat's damage source to fire => undead have already fire damage source with lich queen and I believe adding yet another dmg source (earth) was unnecessary, however keeping Nosferat's dmg source other than death enables his use in the campaigns, where you'd be stuck against undead units with only death/weapons sources
- reverted Vampires' and Elder Vampires' attack sources to death - I believe giving them another attack source (earth) was too unbalanced and unnecessary
- increased Wight's hp 105->130 - he was too squishy compared to death on the same tier, while having worse damage/utility
- increased Dracolich's damage 75->85 - compared to lich on the same tier, wyrm had only 5 damage more while taking 2 slots and having much higher xp requirement - moreover it even had lower damage than dreadwyrm
- removed weapon immunites from Wraith, Death and Wight - it should finally make it impossible to put them in front row and thus enable experimenting with other units
- reverted Death's initiative nerf 40->60 - removing weapon immunity imo is enough

Legions:
- given 10 armor to Anti-Paldin and 15 to Infernal Knight
- reverted Incubus' double attack change cause of base game bug (where on 2nd attack you couldn't defend or attack if there was only 1 enemy left)
- he now has 6 targets attack again but with lowered hit chance 65->50 to be on par with undead's shade
- added fire ward to Pandemoneus - no reason not to have it while the same "demonic" modeus has it

Neutral:
- dragons are pushovers, gave them double HP, 20-50 armor, 1/5 more damaging attacks and higher initiative (40->70) => do not approach without lots of heals or disables
- also doubled XP rewards for their kills
- changed initiative of summon air elemental from 50 to 70 so they act faster - usually they ended up dead before acting, besides imo summons are still fairly useless
- nerfed Medusa's chance to petrify all targets from 60 to 45%, but gave her more hp - in campaign, if you don't have enough ranged damage and fight parties with 2 medusas - you're permanently petrified (for example in dwarfs' 3rd mission)

- changed final boss for each of the 4 main campaigns to be more difficult:
- Demonic Uther (Empire & Legions): initiative 65->90, armor 0->50, hp 1500->2000
- Nhiddog (debuffed): initiative 50->90, armor 0->50, hp 2000->2500
- Taladrielle: initiative 60->90, armor 0->50, hp 800->1300 (it's really tough fight on paper, but as undead you'll have plenty spell debuffs)

Any feedback is appreciated.

Mod has been released: https://www.moddb.com/mods/d2-nevendaar-rebalanced-20

Shameless bump.

Haven't played with the mod, but played a lot of D2 overall:

About Alchemist, can't really agree. I honestly find it 50/50 on whether to use her or Druidess. In many scenarios, Alchemist is actually preferable. The cure on Druidess loses a lot of effectiveness simply because the Druidess goes first due to initiative. Meaning she can't cure statuses on the other units. If you wait, you lose on the damage buff for the first turn and risk getting her paralyzed, meaning she still doesn't get to cure. Alchemist's super low XP requirement also means she levels pretty much non-stop and gains a lot of HP fast, allowing her to actually take a few hits + heal from leveling up pretty much every other fight, which is also a quite strong factor by itself. And lastly, the druidesses' buff becomes overkill in a lot of cases. A single level on a Son of Ymir means she is already not buffing at full effectiveness.

Tempest Giant - Elder one: They definitely need something. I'd probably give Elder One a low chance of paralysis, like 35%. Source air if possible. There isn't a single scenario where 2 Hermits wouldn't be better.

Flame Caster - I'd just equalize his HP with the Forge Guardian. Always found it weird he has 25 less HP than Forge Guardian.

Human fighters - I'd be really careful about bumping the HP of the ones that have armor. Don't forget about armor stacking. Slap a Banner od Fortitude on them and you're already at 50 armor. Not to mention they can also get up to 9 armor from levels.