Eh... Him being 20 something in the early 60s and his 'daughter' being a fairly young teenager in the late 2000s was already going to feel weird. I'd just as easily find out she was actually his granddaughter, which would mean there's no particular problem there (since we have no exact date on his death, we can assume he had enough time to have a child before he died).
I do think it was a shame to eliminate him (and Emma, as well) after such a small part.
The X-men movies were set in 'the near future' in 2000 so trying to date them is far trickier. Potentially if he was only 16 in First class and Syrin was only 14 or 15 in X2, he could be in his forties when she was conceived. Seems more than plausible.
Well, he really didn't seem 16 to me there. But if that was the case, then, yeah, ok.
I do think it was a shame to eliminate him (and Emma, as well) after such a small part.
Well, the actress they cast as Emma was pretty disappointing -- she sure looked the part, but her performance was lifeless and bland. So it's no wonder they declined to bring her back.
Not liking the actress doesn't mean they needed to eliminate the character, though. It's not like they haven't recast things before - and even if they didn't want to use her right now, they could've written her out in a way that didn't involve death. (Or just completely failed to mention her at all...)