Its really a matter of opinion. Personaly I favor undisputed. You may not have beat the man who beat the man, but you've pretty much beaten most of the best fighters at that weight. Very subjective though.
Well... normally, if you unify all titles, you have to become the lineal champ somewhere in the process. But you can become the lineal champ despite not unifying all the titles or defeating the undisputed champ. Like if you defeat Zsolt Erdei, you will become LHW lineal champ but not the undisputed. Undisputed has to be considered more valuable since you can only become one if you unify the alphabet titles AND the lineal title or if you defeat someone who has done that before you.
The concept of a guy being "undisputed" but not linear is pretty contradictory. You had Mike Tyson being called "the undisputed heavyweight champion of the world" for having the big 3 (IBF/WBA/WBC), and then in the other corner you had Michael Spinks being recognized as the linear, Ring magazine heavyweight champion, with it being said that some people consider him the true heavyweight champion. Well obviously it IS a little disputed ain't it?
Exactly! Calling Roy Jones undisputed (and even giving him The Ring title!) when Dariusz Michalczewski became the lineal champ before Roy even started to unify is another good example when the undisputed status is disputed. But on paper, the "legitimate undisputed champ", so who unifies ALL titles, should get the lineal title in the process. How meaningless is the WBO? Well... Roy did unify the "3 big titles" and became the so-called undisputed champ... he just failed the become the legitimate champ since the lineal title was in the hands of the meaningless WBO-champ from Germany (a few knew that Dariusz was actually born in Poland).