I figured each time a new game came out they just wanted to change it up for variety's sake. I believe though that the reason it is blue in JK2 and JA was explained by one of the Raven developers awhile back was being because at the time LucasArts was going through another one of their "be true to the canon" phases, and so basically as a "good guy" Kyle had to either have green or blue, and since he'd already had green (and to contrast with Luke) they gave him blue. Funny thing is that around the time that these games were coming out, they were already breaking that rule in the films.
I'm referring to something Lucas said during the production of Episode II that the "new rule" was that "good guys have green or blue and bad guys have red" (and then, as on the documentary Sam Jackson says "Can I have purple?" and he thinks for a second and then says "you might be able to have purple" or something like that).
The EU always had multiple colors, and that was before Lucas said that. Of course in Episode III, suddenly you have bad guys using blue and green. Another reason might be that it seemed like when the Prequels were coming out that every game featured somebody using blue (a lot of games were prequel based and featured Obi-Wan or Anakin, using blue as in the movies, so I guess blue was on everyone's mind). Personally that made me get a little bit tired of blue, even though it looks cool and was originally going to be the dominant color in the movies (the sabers all started out as white, then they gave vader red to contrast with Obi's blue, and green looked better on the backgrounds in ROTJ so Luke got that color, etc).
When I played JK2 and JA, as soon as I knew how, I used cheat codes to change the saber color to orange for Kyle, to match MotS.
I guess in storyline terms you could make sense of it by saying that if you follow the light side ending of JK1, Kyle has Yun's gold saber, but as he is completing his training and working for the New Republic, then starting to train Mara Jade, he makes his own saber and it's orange. Then after the events of MotS, when Kyle "gives up" on being a Jedi for awhile, he retired his orange saber, and during the events of JK2 he builds a new one that's blue (or was he issued it at the training academy? I forget, it's been so long since I played the single player campaign). Why a different color each time? Depends upon what EU stuff you believe about what causes the color to change. Whether it's a deliberate design thing in the construction or its affected by the color of the "crystal" inside it, whatever. The Prequels lead us to believe that blue and green are really popular but never tell us why (in-universe). Maybe it was a symbol of the Jedi, or maybe those "crystals" were more popular or that technique for construction was more common.
I guess make up whatever excuse you want. I think visually each development team just decided what looked best. I bet if they made a new Jedi game, the color would be different yet again.
The "going through sabers like pencils" thing gets put over in the Prequels, so who knows.