Haven't even gotten MotB, however new prestige classes would add alot. Also, some pockets to pick please! *exports Sleight of Hand maxed character and picks green guy*
Before anything, as I've said, I do not have MotB and I may have missed some stuff in original game as well, had it in a close time and completed it only once (on my way to second). So don't boo me if some of them already exist or so.
Anyway, here goes my suggestions (with a little description for those not familiar)
Mystic Theurge: You get 3rd level arcane and divine spells to get this. After that BOTH your arcane and divine caster level increases in every level. I'm not sure how they missed this prestige class in the first place, then once again in the expansion.
Drunken Master: Let those bewerages work for wendersnavens sake! This Evasion-as-class-ability-for-requirement prestige class lets you to drink like a demon and unleash alcoholic hell upon your enemies as you trip and stumble! Give monks a chance!
Master of Chains: Of course this needs Chained Spike implemented first. But this prestige class sooo many abilities that it makes playing a fighter less boring and more tactical and active.
Tempest: Two-weapon fighting galore! (or as an alternative
Twin Sword Master by ~themaelstorm on deviantART )
Contemplative: A cleric/paladin (actually anyone with 13 knowledge (religion) ranks who has contacted a deity's agent.. or a deity) that keeps getting caster levels along with many monkish benefits like being immune to diseases, poison, having SR, slippery mind etc.
Holy Liberator: A chaotic good prestige class that welcomes most core classes with a few paladinish abilities (charisma to saves anyone?), a celestial companion (as in, say, a celestial dog) and few divine spells like a paladin again.
Hunter of the Dead: Name speaks for it, although some abilities would need to be changed to be useful in game (like True Death, which forbids a body that was slain by the hunter from raising as undead).
Sacred Fist: Hello, I am a few-divine-spell-casting monk. Nice to meet ya.
Templar: Hi and I am a few-divine-spell-casting warrior class. Me crush puny kobolds!
Elemental Savant: Hi hi, I am a wizard who specialize in an element and eventually become an elemental creature of the chosen type with of course better casting of spell in that element as well.
True Necromancer: Hello, unlike that pale-as-my-backmaster, I DO cast both divine and arcane spells of necromancy. Undead around me are stronger, I have continous magic progress and create loads of undead. Plus, I have this gothic name!
And about current classes:
Palemaster: hey, that arm gave +4 strength and 4 types of touch attacks!
Dragon Disciple: Give'em their size bonus! And, different dragon types as well!
Also I would love following to be considered:
Grapple: Implementing this would be nice. Although, graphically, I do not know how it would be possible. But there are many stuff related with it, it would be nice (size bonus if nothing else).
Summons: 1 Summon per character? That sucks. Palemasters should have a few undead around for Velsharoons sake! I wish it was like 1-creature-per-spell-type. So say, 1 from undead summons, 1 from class summons (if any) and 1 from summon creature spells for a max of 3.
And please, give us a few choices to summon from :/ I don't want to summon a boar or bear with my ebil gothmaster character. I mean.. He wields a schyte :/
Feats that may be nice:
Energy Substution feat (metamagic): Allows you to change the energy type in a spell. Say, cast a cold damage fireball (well, yeah, a cold ball <.<

. Hint: Sonic is the way to go, as is the opposed element with elemental-subtype creatures.
Green Ear, Requiem and so on: Allows your bard music to effect plants, undead and other creatures that are immune to mind-effects normally. These feats require perform skill of various levels (Requiem, that allows undead to be effected, requires 12 Perform for example)
Hamstring or something similar: Sacrifice some of sneak attack damage to cause a different effect, like slowing or ability damage.
Dual Strike: Allows you to strike with two weapons as a standart action, you make a single roll with your highest attack bonus-4.. I think it's -6 or -10 if your off-hand isn't a light weapon.
Augment Summoning: Makes your summonned creatures stronger.
And...
(LIMITED)WISH, TIME STOP AND IMPRISONMENT (+FREEDOM) PLZ. <.<