I'd like to first say that I know that the authors endeavored to convert MotRD to 3.5 as best as possible, and in many ways their work shows in the book. However I disagree with some of the choices they made about certain rules, and other rules make no sense. So I decided to try and make a set of alternate rules, which are presented below.
1) Arcane spellcasters do get bonus spells for a high ability score, INT for Adepts, Metaphysicians and Occultists, and CHA for Charlatans. I see no reason why they shouldn't get these bonus spells, other than the fact that they didn't have them in 2E. Considering that spells take longer to cast, and that their is a chance of failing a DP check, I imagine most PCs will not cast as many spells, but for those Adepts who will, give them bonus spells.
2) The book never says how many languages a PC starts with. In a typical D&D campaign it depends on race, so I decided to base it on nationality. You start speaking your nationality's language(s) plus a number of bonus languages equal to your INT bonus. For example an American with an INT of 14 would start with English, plus two other modern languages. A character from Switzerland, might start with German, French, or Italian, or with the DM's approval could speak any two of the languages. In areas colonized by the Great Powers, such as India, a native PC begins with his native language and the language of the country which colonized the area, plus bonus languages.
3) The Shootist is now called the Marksman. (The title applies to either gender.)
4) The Occultist should gain bonus spells for specializing in a school of magic. He also chooses two (not one) opposing schools, neither of which may be divination (see the PHB p. 57 for details).
5) Parsons may select any religion (not just an ancient one) for the Bonus Skill Focus feat at 3rd level. Parsons are not prohibited from taking combat oriented feats, unless their religion specifically forbids them to.
6) Mystics, mediums and spiritualists should all be able to turn/rebuke undead (depending on alignment). See PHB p. 159. All undead in Gothic Earth get +1 Turn Resistance, as they would in Ravenloft.
7) Criminals (and any Prestige Class with the Trapfinding Special Quality) do get to use Search and Disable Device to find and disable magical traps. However the DC to do so is increased by +20.

9) The Performer gets Sleight of Hand as a class skill.
10) Lycanthrope Hunter: the "Special" qualification for this PrC is incredibly vague. For the encounter to qualify, the PC must know the NPC is a lycanthrope, and fought it (but not necessarily defeated it).
11) Undead Hunter: the "Special" qualification for this PrC is incredibly vague. For the encounter to qualify, the PC must know the NPC is undead, and fought it (but not necessarily defeated it). The "Favored Enemy" Special Quality functions exactly as written under the Ranger class in the PHB. This Special Quality does not give the PC knowledge of undead; that knowledge comes from the Knowledge (Forbidden Lore) skill. The PC must still make skill checks to see if he recognizes weaknesses of undead.
12) Academician should be replaced with the Search skill when searching libraries for information.
13) The Connoisseur skill should be a feat, which grants a +2 bonus to Appraise and one Craft skill.
14) The Self-sufficient skill should provide a +2 bonus on First Aid and Survival checks, not Heal and Survivial.
15) Find Familiar feat: no mention is made of the costs involved in using this feat. Each time a familiar is summoned, the PC must spend $50 worth of materials. The familair summoned is a dread familiar; there is no DP check.
16) Bows should not be considered Simple weapons. They should be either Primitive or Exotic Weapons. Crossbows should be simple weapons, except the hand crossbow, which should be Exotic.
17) An Adept who fails to successfully copy a spell into her spellbook, but has successfully classified the spell, may not attempt to copy the spell until they gain a rank in Knowledge (Forbidden Lore).
Any comments?