Regenerating health - Yes.
Iron Sights - No.
Seriously, I don't get all these people who think that iron sights would ruin a game. If it was the only way to shoot, yes, that would be bad, but as an option, it would be nice. You don't know how many times I wished I could look down the sights on the SMG to get a better aim at some Combine who were some distance away.
Regenerating health, cover-based mechanics and a bad ending would have a much worse effect on the game than looking through gun sights.
Besides, it doesn't really matter anymore anyway because VALVe doesn't give a shit about the Half-Life series anymore. I thought they did. At one time I would have dissed any notion that they wouldn't make a sequel. But since Episode Two's release, they've made a new franchise, made a sequel to it, added umpteen million TF2 updates, got a sequel to a game released at the same time as Ep2 and now Counter-Strike is going to get a sequel before Half-Life 2. Really, I have just lost all interest in the series.