Don't be. Sure, Raiden was annoying but he still succeeded in doing what he was supposed to: make Snake look even cooler. It really was largely a game about Snake despite the playable character being Raiden instead of Snake. That said, I doubt SE can really pull off the same trick Kojima did, at least not as well as he did.
I see something similar happening here. The game will largely be about Lightning etc but it will involve parts where we don't play as her too.
For the record MGS2 is one of my fav MGS games so I didn't mind, besides Raiden was hated for the silliest reasons (and some valid reasons), and I liked the whole Rose/Raiden relationship thingy.
All hail the KING, Andrespetmonkey