I agree completly and totally with you. I think we can all agree that Hero-of-Time Link is totally awesome, and references are cool, but they should either outright say it or leave it alone.
I did see a difference between WW and TP's handling of it though.
In TP..we had a ton of references.." tales are told all over Hyrule of the legendary hero and you bring them all to mind" ( Renado to Link ), Impaz recognizing Link by his clothing and the biggest offender in my mind was the Hero's Shade. He makes vague references to being a hero, he's dressed like a knight and haunts the castle area..he's missing an eye.
So instead of talking of us talking about Hero-of-Twilight Link: everyone wants to know if the Hero's Shade is OoT/MM Link, if he is: why is he missing an eye? Did he become a knight? How did he figure into Ganondorf's execution, how did he spend the rest of his life? All they did was make the new hero seem unimportant to us fans of OoT.
WW in contrast: They directly referenced OoT Link. They said he disappeared and was not there to fight off Ganon. So we got some sort of closure..and WW introduced a new hero: he got compared to the old, but it was outright and IMO the HoW stuck in my head because of that. He was similar to the old, but different.
I am really not a fan of seeing another HoT game...I honestly don't think they can capture that same feeling...I felt they tried in TP..but failed. TP Link had too much personality, he was his own person, with definate feelings and desires apart from the player, unlike the pretty much emotionless HoT.