Skill based magic system, not fire and forget!
Magic causes fatigue
The one thing that really bugged me about magic in GURPS was the DX-based "throw" skill check needed to hit with lightning bolt & similar spells.
GURPS Magic (at least the 3/e one) had lots of cool options I liked to use. It also had some alternative systems that can be good for some campaigns. I liked the Alchemy system.
GURPS Voodoo, Spirits, & Cabal had some interesting looking alternative magic systems, but I never got around to buying them.
I guess this is standard in 4/e, but if you're still playing 3/e, it's a good idea to base hits off ST & fatigue off HT. Besides the other benefits, it keeps all the wizards from being body builders.
Armor as damage reduction
It doesn't really matter where in the process armor gets figured in. What matters is, given all the factors, how much damage potential character A has against character B.
That said, GURPS has one of the best implementations of applying armor to the damage roll.
(Personally, I still prefer something like Rolemaster Arms Law in which "to hit" & damage are determined by a single roll. But I'm crazy.)
Weapon ease of usage dependent on strength
I liked the way they separated weapon skill from weapon. (You had the stats for using a staff with your sword style (with your sword skill) v. using it in normal staff style (with your staff skill).)
Ease of racial templates compared to trying to sandwich a race into an EL category
In 3/e, at least, the "race" books gave different costs for advantages if they were part of your race package than what the cost would be if it were just a normal advantage. I found that problematic, so I ruled that if a racial advantage was basically the same as a normal advantage, it cost the normal cost.
Possibly my favorite GURPS campaign was the one in which the GM allowed everyone to create their own race.
Skill based system as opposed to levels
These days GURPS skills are too narrow for my taste. (Although some people get around this with bang skills: Sword! Science!)
I find a game like Lejendary Adventures preferable. It's skills are much broader than GURPS skills yet not as broad as classes.
GURPS has levels. It just calls them a "point total" & they're much smaller than D&D levels. (You typically start at 100th level.)
No assumed level of magic items necessary to meet CR of monsters
Yeah. (Although, I've never found the D&D assumption that PCs would have a certain amount of magic items to be a problem, even though I tend to be very stingy with magic items.)
On the other hand, I found it more difficult to determine how much of a challenge a monster would be than it was in AD&D.
Combat looks like it might be slower
This is a big dilemma I had when thinking about running GURPS again. The advanced combat system with all (or, at least, most of) the options is very good & ends up creating important trade-offs between the different equipment & tactical options.
But, it's also very complex & slow to play. You can scale it back to something that plays fast, but then certain equipment & tactics suffer. (e.g. A two-handed sword almost needs all the options in play to be practical.)
Automatic failure on a skill check (3d6) role of 17 or 18
Yeah. Although, to me, the crit rules are even more annoying.
In the last GURPS campaign I ran, I switched to an open-ended d20 roll with no automatic failure & crits being determined by how much you made or missed the roll by. It seemed to work pretty well.
When I was considering trying GURPS again I was thinking of using something along the lines of D&D3e's crit threat/confirmation roll for failure with high skill levels & crits. (A mechanic that GURPS already used for malfunctions when using some weapons.)
May be too generic to best reflect the flavor of D&D style fantasy
Check out
Caverns and Creatures. It's a sort of intro to GURPS for D&D players.
I think GURPS has a very different feel than D&D. (But then, when I was playing it, I wanted a different feel than AD&D.) It feels closer to real life to me than D&D does.
Also, check out
UMana.