GURPS is hands down my favorite system. I love looking at other systems and rules, but I always compare them to GURPS and they have always fallen short against it.
That said there are some things that erk me a bit about GURPS ... like Disadvantages. I like the idea of disadvantages. I like that they give a way to build more rounded characters that aren't just a collection of "ways this character is better than others". But often I find that disadvantages are taken not to fill a concept, but for the points.
When I come up with a character concept, I think of the character's strong points first. If there is some sort of "tragic flaw" or other drawback it tends to be one thing, or a few very closely related things. But once it comes time to build the character with a point budget, I will look for additional disadvantages in order to have the points to spend on the character's strengths.
Even the official templates seem to reinforce this approach. Dungeon Fantasy, Action, and Monster Hunters have templates where the full disadvantage budget has been spent.
Now maybe, some GMs have no problem keeping track of all of their player's disadvantages and can make sure that they all come up in play and are worth the points they got for them, but I must admit that if each player has a half-dozen or so disadvantages, I can loose track.
And in play, characters tend to focus or become known for one or two disadvantages, while others become little odd-ball traits that the character has... but don't feel like they define the character. When a disadvantage is "working" it can be THE defining trait of a character, but again this tends to be one or two. The rest of the disads are forgotten till they come up, then just serve as minor annoyances.
This leads to another issue with disadvantages, the value of a disadvantage may not reflect the actual level of difficulty or interference that it causes. Even within the same campaign, a disad might go from something common to almost never coming up. Such as the character with a fear of water and an adventure hook that leads the party from the ocean to the desert.
Other systems avoid some of these issues by doing things like limit the number of disadvantages (not just the points, but the total number), one "major" and two "minor" or something like that. Another interesting option is to not give any points for disadvantages, but instead reward players with bonus character points when a disadvantage comes up in play.
Still, I do like the idea behind giving points for disads. The real solution is to do something like "narrative" character creation or the character interview to create a solid concept before any points are stent. Then make sure that every disadvantage is justified by the character's concept and background. Of course, this takes much more time, and is sort of the antithesis of the template system.
I wonder if a more guided interview customized by genre might not be a better system for GURPS genre books than just lists of templates....