I gotta say, X-men FC made some scenes in X3 actually better.... and deeper (like mystiques depowering, and charles "death")
also... it's not hard to fix some continuity...
1) Moira (simply have the one in X3 be FC's daughter or grand daughter) she's named after her, and begins a close relationship with Charles.
2) In X3's opening scene, Xavier is lecturing Erik about "power corrupting" and Erik says something almost suggesting that he was evil at one time, and is now "rehabilitated" So Xavier and Magneto could easily have become close again in the 80s (they'd sort of have to be anyway to make there friendship seem as deep as it did in the trilogy). In the comics this also happened several times, Magneto has also lead the x-men several times.. (This would be interesting to see in a FC sequel)
3) during the "re-friending" Magneto helps charles (using his powers) build a new cerebro in the mansion sub-basement
4) during this "re-friending" magneto could also fashion a device to help charles walk (thus explaining X3 and XO wolverine
5) the XO cyclops cameo could still work (still doubt the baseball player was him.. he just wore glasses... they werent red)... so his (as well as storms) are sort of throw away cameos (sort of like Dani Moon Star, Colossus and Jubilee in X1)
6) Emma frost in XO was simply just named Emma... Kayla had the last name Silverfox, so one would assume Emma has the same last name... she also was not a telepath, and her diamond form was visually different then Emma's in FC.
The only thing that simply just truly doesn't fit, and can't be undone, is that in X1 Charles tells wolverine he met Erik when they were 17.