[Rygar]

First of all, why is no one listing Mage as an unpopular class? I hardly ever saw them in groups leveling up.

I like the charm changes mentioned but would add a few spins:
Enchanter = Humanoid
Necro = Undead
Magician = Elementals
Shaman = Constructs (such as muddites / golems, stuff with an 'earth / clay' type theme)
Druids = Animals
Bards = Remove charm all together or level cap it to <35

Class Specific help:
Wizard - Basically all that has been mentioned with crits and better sustained DPS. I think lore wise they used runes and stuff to enhance items and use for protection. Would be nice to allow them a specific tradeskill such as 'Rune making'. Could create some sweet self-only gear, as well as some tradeable pieces (maybe even a DA idol type of thing, some focus items, or FT1&2 type items... maybe FT3/4/5 self only items). I think also allowing them to cast +mana buffs that are superior to GoB would be a good idea (say +300 mana), even with a small +2/tick mana regen that is stackable with all other spells. I think they got this in later expansions.

Mage - Improve monster summoning, should be able to inherit some abilities with it. Could make for some amazing pets. Also improve summoned / temporary items. Summoning even a 10% haste item at lower levels could make them more valuable for newb groups, and even improve haste summoned items at higher levels (say 30% haste at level 49, I dare say even 40% at level 60). Adding charm to elementals (again added later) and adding more elementals to zones could be a huge help. Unresistable slow line of spells against elementals also fits well.

Ranger - Always thought they should have a pet line of spells that can improve their bow abilities (Eagle = better accuracy, Wolf = more damage, Snake = DoT / Snare). Pet would do some melee dps as well. Spell line to add procs to their bow, and self-only haste spell just affecting bow speed / atk power.

Paladins - Should really have fear immunity, big raid utility on some mobs there. Group buffs that are in the 'Bane' line of spells against undead. Would be cool to have a pet that is a squire to help do some DPS. Squire may also be able to absorb a % of damage for the paladin and maybe can have a chance to sacrifice himself to absorb the killing blow against the paladin.

Shadowknights - I always liked these guys, not sure what to change exactly. Higher proc lifetap line could help to self heal and mitigate damage. Maybe have a spell that absorbs life from group members like a reverse DoT to help in tanking big targets. Could make for some synergy in group construction.