I think Shepard needs to be (and will be) the protagonist throughout the entire Mass Effect trilogy. I'm a relatively recent convert to the ME experience myself and having such a heavy emotional investment into the Commander and his crew, I would be shocked and deeply dismayed if all that was set aside just so BioWare could "reboot" things for another RPG level climb.
For the same reason, I won't be happy if most or all of the companions in the original game aren't around for the second. Those relationships were a big part of the original game and casting them off for the sake doing it all over again would be a big mistake. Given BioWare's history I don't think it's terribly likely to happen but I'm going to stay just a wee bit nervous about it until we have a better idea of what's actually going on.
For the same reason, I won't be happy if most or all of the companions in the original game aren't around for the second. Those relationships were a big part of the original game and casting them off for the sake doing it all over again would be a big mistake. Given BioWare's history I don't think it's terribly likely to happen but I'm going to stay just a wee bit nervous about it until we have a better idea of what's actually going on.