The primary reason I chose the changes I did was to make something that was quick to prep for and easy to run, but was still compatible with E-Tools and didn't take a whole lot of mental gear-shifting on the part of the players. Of course, that was before I made the discovery that Windows Vista and E-Tools don't get along — especially when it comes to printing up stat blocks, which is about 70% of what I want E-Tools for! However, when polled, the players preferred that I stick with this system and just find a workaround for the E-Tools printing problem, rather than going all the way to Saga, apparently more because of comfort with 3.5 than anything else.
Also, on Saturday, the time I had intended to put into game prep largely got eaten by a call from my parents for assistance with grocery shopping; so by the time the game started, I had to just go with the module more or less straight as written with only cosmetic changes; the monster stat blocks remained unchanged. That actually turned out to be quite fortuitous for jamesbarrett's rogue, who would have been darkmantle-chow if it weren't for that "triple 1st level hit points."
But last night I started going through the module and actually "converting" the critters over to my new 3.5/Saga hybrid, as much to cement the encounters in my mind as for any mechanical reason. "Spot" and "Listen" got chucked for "Perception," saving throws got tossed in favor of defense scores, and so on. Although I didn't get through the whole module, I did get pretty far, pretty fast. Not quite as fast as simply copy-and-pasting from E-Tools, perhaps, but fast enough and with more flexibility to simply add abilities to give the critter more options if I felt like it.
For instance, a type of local raptor, the "razorcrow," is described in the module as having the same stats as a hawk in the Monster Manual, and there's at least one encounter in the module where the players are almost guaranteed to go up against couple of them. Unfortunately, the hawk as written is kinda dull ... all it can do is fly and attack, and not an especially scary attack at that. So I gave them a new ability to represent the harrying effect often associated with the attacks of flying beasts. It took maybe three minutes and suddenly made the encounter much more than the pre-ordained "race to the bottom of your hit points" fight it would have been before.
I realize that this approach is closer to the "4E" way of doing things than the "3E" way. In 3E, monster types are basically like character classes, and you have to figure out things like the monsters' skill points, their effective levels, and so on; but for all the things I dislike about 4E, one thing I do think they got right was the understanding that for the most part, monsters don't actually need all that stuff. Their job is to show up, give the characters a fight, and either die (most commonly) or force the characters to surrender/retreat (less commonly). If a player wants to make a PC version of a monster, then you need to figure out some way to translate its abilities into something players can use without breaking the game — assuming you let the player do it.
Point is, most of the time, the players don't see under the hood. They may figure out over the course of a fight that a creature has an AC of 17, but they don't know if it's because the creature has 17 Dex and 4 points of natural armor, or if it's because the creature has 12 Dex, 3 points of natural armor, and a +3 ring of protection unless they're going around casting detect magic in the middle of combat. And frankly, a player who would go around trying to reverse-engineer the stats of creature in order to somehow audit the GM is probably a jerk anyway and you're better off without them at your table.
This realization gives the GM a lot more leeway in terms of making adventures that actually challenge his players. If you want them to go up against a monster that's hard to hit, but that "mathematically" you can only get up to AC 13, go ahead and give it +5 more points of AC. You're the boss! Not in the middle of a fight, mind you — then the players will be well within their rights to know how the critter did that — but when you're building it in the first place. "Compared to the rank-and-file orcs you've been fighting, this guy is a vicious brute who has an amazing ability to knock away your blows."
The key, I think, is to make the ability something that makes sense in the context of the story. A big, vicious orc that is hard to hit makes sense. A big, vicious orc who turns incorporeal doesn't (unless he has a magic item or something, that the players will very likely want to claim for themselves). This is one of the things that bugs me a lot when playing LotRO, that the mechanical and narrative effects of monsters often don't seem to match up. (Seriously, a wolf's howling halves my running speed? What sense does that make?) But assuming an ability is within the realm of possibility for a critter, or at the very least has some explanation, most of the time players should be cool with it. This is especially true if you allow them to come up with ways to bypass it or turn it to their advantage. Sure, the big, vicious orc has an AC 18 because he can knock away blows — but that won't help him much against a sleep spell, now will it? *whump*
The other thing that I've been doing is being more flexible about things like spells. Instead of figuring out a monster adept's "spells per day" and making a list of what spells they can cast, I simply come up with an ability I want the adept to have, how many times they can do it (or whatever other restrictions it has), and describe it as if it were a spell. "The lizardfolk shaman offers up guttural prayers to Jhebbel Sag and foosh! healing energy infuses his minions!" Was it a mass cure light wounds? Was it some variation of aid? Who cares? The players know what happened — the shaman healed the minions — but whether it's a 1st, 3rd, or 7th level spell doesn't matter. Mass cure light wounds is a 5th level spell — "by the rules," your lizardfolk shaman would have to be 9th level to cast it. Fine and dandy if you've got a higher-level party, but what if you want your 3rd level party to go through an encounter with a minion-healing lizardfolk shaman?
Being the GM means never having to say you're sorry. ;) And if the players ask how a 3rd level shaman is casting mass cure light wounds, you can always smile and say "Become a shaman of Jhebbel Sag, and you'll find out!" As long as at the end of the day the players are still having a good time, you've done your job.