I was never much of a fan of Owen- he was an interesting character, and a realistic horrible slimy little so and so for much of the time, but the attempt to turn him into someone more sympathetic didn't really work for me, and after his death and return, I don't think any more could really be done with the character.
Tosh certainly had more potential, and in many ways I'd rather have seen her stay and Gwen killed off- though if Gwen died Rhys would no longer have a part in the show, and I think it would be poorer without him. Rhys is a lovely character and surely deserves better than Gwen though!
I really like Ianto and hope he survives this series- he didn't feature much in series 1 (certain episodes have been forcibly wiped from my memory!) but I thought he was great in series 2, loved the dry wit and one liners. He needs to keep those in this series. I don't mind the idea that he doesn't usually go for men but still fell for Jack- after all, people are far more complicated than simply saying they fall in one category or another. I do worry that Jack will break Ianto's heart though!
Torchwood still resolves primarily around Jack and I'd like to see that change- he's an interesting character, but since I enjoy Torchwood and would like it to run for a long time, if that were to happen sooner or later Jack would have to be written out (not necessarily killed off, but sent away somewhere else for a while, maybe returning after a break of a few years claiming he's lived 3000 years off time travelling while everyone else has only lived 2, or brought back in a far future set spinoff?)- the character is ageless, but the actor is not. So the rest of the cast need to be strong enough to carry the show. Right now I'm not sure they are, but there's certainly room for some new characters.