Matrix sequels are relatively better. They at least make a slight degree of sense with regard to the first film, even if they were better left unmade.
Highlander sequels... Well, Highlander 2 is a good enough film as long as you pretend the first film doesn't exist, but it's all downhill from there. Not so much 'There Can Be Only One' but 'There SHOULD Have Been Only One!" Connor's the only immortal left alive at the end of the first film, so everything that follows isn't even possible.
This one is a real big toss up. On one hand I actually enjoyed Highlander 2 because of its amazing cast, and it was so bad at times it was kind of good. I also haven't seen the third film.
With the Matrix sequels it still had a decent cast (Henry Lenix, Laurence Fishburne) they could have easily been edited down to one film. Plus I did not like the ending to the second one which kind of ruined the whole trilogy IMO.
I think I may have to say the Highlander films just barely edge out the last two Matrix films for me.
Matrix sequels are better, without a doubt. At least the Matrix was merciful enough to finally end. ;D
Granted, the Matrix Reloaded was so ridiculously tedious that it managed to make a car chase boring... but at least it wasn't quite so openly and brazenly dumb. Which is more than I can say for Highlander: The Source, which had more plot holes in 10 minutes than both Matrix sequels had through their entire run. It's just a truly awful and deplorable film.
Even leaving that out, I'd still go with Matrix, even though neither should have had sequels made. Highlander was designed to be one movie, and utterly failed to get around that until the TV show. Matrix at least had a direction after the first film, and wasn't wasting several films trying to get around the ending to the original. So...yeah.
Both have a (originally) lowly hero who eventually becomes essentially the most powerful being known (the "ONE"). Both original movies rocked face. Both had BAD sequels.
I never though I'd say these words, but the Matrix sequels have got to be the winner here. (Even comparing the original movies Matrix wins, though barely). ReLoaded wasn't all that bad, it was as if it distilled the essence of the first Matrix yet losing something in the process. We get obtuse philosophy about truth and inevitability mixed with long fights and chase scenes, some good, some boring, most dragging on too long for anyone trying to fight Neo, who, according to the first film, was supposed to be able to do ANYTHING he could conceive in the Matrix. Revolutions was awful I thought, bringing the fight out of the Matrix was bad enough, but now Neo has powers in the real world for no reason? EHhh....long robot fights....
The Highlander sequels were much worse. Completely incoherent. The story began and ended with the first movie! Instead they just put the characters in a completely different continuity in part II (The highlanders were aliens? And they knew each before they came to Earth...) and in part III (carbon copy of the original, abandoned the previous two movies' continuity). I even saw the fourth one, which merges the movies with the TV show, and was awesomely bad. I think there's a fifth one called The Source but I'll pass