Rules Changes
Fixed Skill Checks
Skill checks work differently in Maugeter to the way they work in NWN or D&D. Skill checks are "static", meaning if you have a specific, fixed level in a skill (ranks+stat bonus+modifiers) or higher you pass, and if you have less then you fail.
There are several reasons for this. The first is that the element of randomness which makes skills checks an exciting and interesting thing in a pen and paper game simply does not exist in NWN. There is no tension in clicking on a conversation option and seeing whether you passed or failed. Secondly, the availability of quests or items may depend on the outcome of these skill checks, and introducing a random element is detrimental to the "fairness" of this. It isn't good game design or DM policy to decide whether a player gets something important based on a random outcome. Thirdly, as demonstrated in the Official NWN Campaign, writing dialogue which doesn't allow you to take the same skill check again and again until you pass is tedious, and this system avoids the problem; if you couldn't pass the check the first time you won't be able to pass it on further attempts either.
All Skills are Class Skills
All skills are class skills for all classes. This is intended to give you more freedom in the concept of character you choose to play. In most cases it's not hugely advantageous to take inappropriate skills. Remember the effect that the Armour Check Penalty has on most Rogue skills, for example.
Rest Restrictions
Resting in Maugeter is assumed to be a night's rest. You can only do this in a safe, private area. Within the city, look for inns or (occasionally) abandoned houses to rest in. You can buy your own property or rent your own room if you like. Outside of the city, you can rest at organised camping spots.
Whenever you rest, you will dream.
Experience Points are only awarded for Quest Completion
You don't get experience points for kills in Maugeter. You get them for completing quests. You don't get XP for completing a quest which is lower level than your character - the number in square brackets before a quest's name in the journal tells you its level.
Experience points are awarded in this way to ensure absolute equality between different approaches. Hanging around killing respawning enemies is not an advantageous strategy. If you'd rather sneak past enemies than defeat them, you won't be penalised for it. Perhaps most importantly, you will never have to wonder whether you can hand in the quest THEN kill the quest giver for maximum gains. Put it out of your mind, and focus on the task you've been given.
Respawning (Fate Points)
You can respawn a limited number of times. The limit on respawning is called "Fate Points" (after WFRP, obviously) and this total is equal to 1+Wisdom Modifier. Halfings (and goblins) receive 1 additional Fate Point, and Bards double their total Fate Points after other modifiers. Your available Fate Points reset each time you level up.
The Goldinator
Merchants within the module will not buy anything from you. However, you start the module with a device called the Goldinator which will buy any sellable object for 95% of its value. It does this so that if you choose to specialise in a weapon style which doesn't match the pattern of items that drop in the module, you can recoup almost all of their value and buy a replacement which is more to your liking. There is currently no in-character explanation for the existence of the Goldinator, and I am loathe to include one because it would likely be unsatisfying.
Ability Buff Spell
The ability buff spells (Bull's Strength, etc) have been changed from the rather silly 3.0e 1d4+1 to 3.5e's much more sensible +4.
Identification
At the moment, magic items are automatically identified when you pick them up. I may change this in future.
Summon Creature Spells
Dire animals, they're pretty boring, right? Well, actually they're pretty cool, but once you've played a few spellcasters in NWN you might yearn for something with a little more colour. In Maugeter the Summon Creature spells have been reworked so that you can summon something more interesting.
Wizards, sorcerers and clerics summon elementals of various types. Druids and rangers summon animals appropriate to their environment.
New Familiars and Animal Companions
This one has its own page.
New Cleric Domains
This one also has its own page.