While I don't collect MOTUC myself (exclusively due to the expense in doing so, i.e. I would if I could) I do enjoy following the bios posted and would have to say a couple of things about the Son of Keldor/Skeletor.
First off making him a new character just plain makes sense, making Skeletor's son some pre-existing character that time travels to the past has potential to make He-fans' brains drop the clutch.
Second is that while I would agree that Voltron's Prince Lotor does happen to reseble Keldor more than he does King Zarkon most crossovers just get plain wierd (as an example in the 90's DC and Marvel did some crossover stuff and would up fusing Batman and Wolverine into one character).
Third I think that giving Evil-Lyn a son adds another interesting aspect to her. From reading BG Evil-Lyn's bio online I get the feeling that Skeletor's son has a lot more to do with her story than Skeletors'.