I agree with Aeara because Link's descendants would be highly unlikely. Why? Because Link's descendants wouldn't be random children because the Gods would always look after them because of his deeds. Well that's just a basic assumption. Also, if Link did have descendants they would all pretty much be expert warriors because he would teach his children how to fight and so on.

I also think it's cruel to think that all Links and Zeldas have two different lineages, cutting off any possible 'interaction' in the past, before Wind Waker.

Also, if you look throughout OoT, we can find many... MANY instances where Link is portrayed to be simple minded. For example, with the Ruto marriage situation as you mentioned and so on. I think the game makers wanted to match link with a person of his mind set, someone as simple as him but as ambitious as well. Malon seems perfect. Link and Malon growing old on a farm with Epona and some cows is ideal. Also, Epona, one of Link's best friends is from Malon, already developing a strong link that binds them two together.

Good write ReRush, very good insight and excellent presentation.