Mmmm, NWN is pretty far away from 3.5, as far as I know. The unpopular (but actually quite fun) ToEE game was closer, but still missing quite a few things.
Attacks of Opportunity, IMO, take about two sessions to "get" and then become all but a non-issue. They don't come up constantly because once you know what provokes them, you tend to avoid doing those things. So then they don't happen.

It's really a mechanic for determining what is appropriate behavior WHEN ... I.E. the Rogue character doesn't skip past 14 skeletons, 1 ogre, 2 chimera, and a dragon to successfully Sneak Attack the enemy wizard on round 1 ... because there's no reason he can't.
You can then say: "You can't." but that becomes an ad-hoc judgement call on your part as the GM. Why can the rogue walk past FIVE skeletons but not TWENTY skeletons? What if the life of an NPC stands in the balance and the rogue WANTS to get to the Evil Wizard and is willing to have something bad happen to his character (or the chance of it) in order to be heroic and save the Damsel in Distress? What if it's the fighter in full plate instead of the rogue? What about the party wizard? Etc etc.
AoO is a mechanic to control those situations. The Rogue is allowed to get past many AoOs through use of the Tumble skill (another change that will occur when you get rid of AoO), but there is usually a chance that he will fail, and thus be open to an AoO. The Fighter can choose to walk past but he doesn't have Tumble ranks and thus will get attacked more often, but will depend on his HP and AC to protect him from the weak flailings of the skeletons. Etc etc.
Without AoOs, why wouldn't a wizard cast Magic Missile to hit the orc threatening him rather than swing with his staff or retreat? Why retreat when he could instead run right up to a frothing mass of Orcs and cast Flaming Hands in their faces? Etc etc.
Once the Dos and Don'ts of AoOs are known by the players, it's really then a mechanic for incorporating danger into dangerous actions. You CAN run up to the orcs and cast Flaming Hands, but you realize there is a hefty opportunity cost to that action. You CAN waltz past the defenders in a dead rush to get to the girl, but there's a cost on that action. Because of those costs the wizards will attempt to stay protected during spellcasting, the Rogues will devote some of their skill points to Tumble, and the Fighter may choose to take Mobility instead of Great Cleave.
There are arguments on both sides for AoOs as realistic or unrealistic, but in the end it comes down to introducing decisions and costs into the game. Just like Hit Points, Armor Class, Spells Per Day, and Sneak Attacks. Each of these offer options and costs associated with those options ... you have the option to stay and fight, or, knowing you have few/low hit points, you may choose to run because losing all of your hit points means you die. It's entirely gamist, but it's a game. Part of the fun is making choices that have costs associated with them.
As for modifiers ... they should usually be added up before the game begins. The Fighter should know what his Final Attack Bonus is with each of the weapons he uses, and he should be able to roll the dice, apply the number, and be done. Spells and effects are where -I- find most of the problems with Number Creep, but that's a whole OTHER bag of rocks to remove all of the spells and effects that add dynamic in-combat number changes. Bless, Fear, etc.
In general I find that about 1/3 of the time, the players forget some of the in-play bonuses. "I miss ... wait, we've got Bless ... I hit!" etc. But it isn't a big deal. If Bob forgets he's under the effects of Bless for the entire combat, it's just something that happened. If he forgets his BAB, that's a larger issue, but it's on the character sheet, and he should have that filled out before the game begins.
As to the "little things" like Darkness, Rain, Wind, etc. Just remember The GM's Best Friend. The Number 2. If you look, most of the penalties are either -2 or a number divisible by 2. This lets YOU forget everything in the book. What happens when they're fighting in the DARK in a tunnel full of WIND? Just give them a -2 penalty to all attacks and a -4 penalty to "ranged attacks" for the wind speed. Probably isn't right, probably what isn't in the book, but she'll do in a pinch.
I've found that players LIKE stuff like that. Alot. Make it complex. Complex combat != Bad Roleplaying, or even a focus on combat. Build fewer Set Piece combats ... a fight in a sloped tunnel with raging wind ... give everyone a -2 to Attacks, and a -2 to any Skill Check that YOU think might be effected by the wind. Or spice it up and give them a DC 10 Balance check every round or be knocked Prone. What's prone? Ohhhh, a little more severe so maybe -4 to attacks? Sounds about right.
Let THEM (the players) keep track of those numbers. For yourself, just note them on your pad of paper before you begin. If you forget, no huge deal. I actually like to make a note on the stat block ... if I know there'll be a windy gully fight, say, I'll edit the Attack Bonus of my major mook beforehand and neglect to make any Balance checks for the bad-guys and have one or two of them slip and fall at dramatically appropriate moments. Good story, fun gaming, no need to flip through the book repeatedly.
If you can't remember a modifier, just decide if it's Mild/Hot/Extra Spicey and give them -2/-4/-6 and keep rolling.
--fje