Warranty:
Factory - 3 years/36K miles
LINE-X - Limited lifetime valid nationwide
Repair:
Factory - Dealer can't fix it (will probably send out to LINE-X)
LINE-X - Any LINE-X dealer can fix it.
Thickness:
Factory - Extremely thin, only about 50 mil average. It's a slip resistant surface, but not a "bedliner".
LINE-X - About 125 mil on the floor and provides a LOT more impact protection.
Colors:
Factory - Black only.
LINE-X - Practically any color.
Fading:
Factory - Will fade over time.
LINE-X - Standard black will fade, but LINE-X Premium and Xtra will hold their color and gloss.