The trouble with that is were talking different era's, The original x-men were created in the 60's they had there own generation, then we have the second geniuses which was done in the 70's, the 80's had another shake up followed by the 90's and 00's... We couldnt explain that big of a gap between the trilogies... Thats kind of why the x-men movies are set one after the other... Look at it this way If it was better structured, we should of ended up with 9 X-Men Movies...
Think of the star wars trilogys, the idea was this... Lucas didnt want to make star wars 4, he wanted to do a prequel, so he did a prequel trilogy, but now were looking at eras, The prequel Trilogy are now listed as star wars 1,2,3 and they renamed the original trilogy as 4,5,6... the idea was then to make part 7,8,9 - the whole vader clone saga which was only told in novels i think, with Luke Solo or whatever the childs name was of Han and Laiya
So this is how x-men movie history should role...
The Original Trilogy...
X-Men The Movie (rename...X-Men part 4)
X2: X-Men United (rename...X-Men part 5)
X-Men: The Last Stand (rename...X-men part 6)
Then the prequel trilogy...
X-Men Origins: Wolverine (rename...X-Men part 1)
X-Men Origins: Magneto (rename...X-Men part 2)
X-Men Origins: First Class (rename...X-Men part 3)
The future trilogy?
X-Men part 7 - (probably moving towards the creation of X-Factor or being unrelated stories like X-Men: Chronicles or X-Men: Legacy)
X-Men part 8 -
X-Men part 9 -
Now if we take a step backwards a second and apply your idea...
The Prequel trilogy should focus on the characters from the 60's original story... Cyclops, Jean, Beast, Professor X, Magneto, Toad
The Original trilogy should focus on the characters from the 70's line up...
Wolverine, Storm, Sabretooth, Nightcrawler, Deathstrike,
The Future trilogy should focus on the characters from the 80's and beyond line ups...
Rogue, Gambit, Shadow Cat, Psylocke...Sinister, Apocalpyse
So from the movie industry point of view although they havent stuck exactly to the comic time line, they kind of have provided us with the basic line up minus a few characters.