A notable difference from later Basic sets is that ability score bonuses are mostly just those of the original D&D set, although constitution allows up to +3 per hit die (bonuses still starting at a score of 15). Strength and wisdom simply give XP bonuses to fighters and clerics respectively, and dexterity (besides being the prime requisite for thieves) gives a bonus with missiles. The charisma table was omitted, although effects were suggested.
The intelligence table from Greyhawk was incorporated to determine an m-u's spells known. An interesting twist was that even mages of low level (Holmes treated the first three) could make scrolls.
Elves were described as advancing simultaneously as fighters and magic-users, dividing XP equally, with six-sided hit dice -- a bit of confusion cleared up in later versions. The characters in Module B1 included separate elven fighting men and magic-users, and thieves of all four races; all the clerics were human, though.
Per Greyhawk, thieves had no special ability to find traps, and removal was indicated as applying to "small traps such as poisoned needles". Per the original set, traps by default sprang only on a 1 or 2 on d6.
Alignments were five: LG, LE, N, CG, CE.
There were only 70 kinds of magic item: 7 categories with weighted probabilities, then an equal chance for each of the 10 entries in the category. Swords followed the OD&D convention of adding damage only versus foes against which they got a special, higher bonus to hit. There was no treatment of intelligent swords.
The monster list was quite comprehensive; I'm not sure it left out any from the original set, and there were additions from Greyhawk. Besides the hit dice from that work, the multiple attacks and damage dice were incorporated for monsters -- although all characters' weapons still did 1d6.