Not that I would prefer it one way or the other, but what difference would it make if Smith bowed mid-season? Unless they went back to a 13-week block and the Doctor regenerated in the middle of it, it'd functionally be no different than the 4 or 6 month wait we had between Doctors in the last couple go rounds.
What I would much rather have it a regeneration happening that, story-wise, isn't hanging over the Doctor for years. Sure, the Doctor KNOWS that at some point he's probably going to regenerate into another body, but lately I've been sick of this need RTD / Moffatt have had to explicitly tell us it's coming. We thus have it hanging over the viewers' heads for years at a time (almost two years betwen "Planet of the Ood" and "The End of Time", and two years and counting between "The Wedding of River Song" and whenever Smith makes his exit) and I know I'm not alone in being distracted in my enjoyment of the show because of it. Let alone having the Doctor voice his concerns about it - talking about dying doesn't make for pleasant family entertainment IMO.
I hope that we'll have another "Parting of the Ways" or most Classic Who regeneration stories, where the Doctor changes his face as a result of the adventure he's currently in and not some twisted, confusing, and drawn out set of circumstances as we had with Ten and now apparently Eleven. I'd rather our Doctor go out with an "hey, saved the day. Aw nuts, gotta change" instead of a "this has been bothering me for YEARS NOW and I'm FINALLY going to get it OVER WITH!".
Although I love the end of time, I do have to agree with you there. I'd like it to be done dramaticly, maybe with the Master planning this for years and years, but I'd like the dr and the viewers not to have a clue about the regeneration happening until abotu a few months before (the dr not included). Although what I would like to see done is a cliffhanger like they did in the stolen earth where we all thought the doctor was going to regenerate. Maybe have no one in the public know that the doctor is regenerating, and after the episode, have them announce that this is for real, and we all have to guess who the new doctor will be. Maybe do that and then split the series in half so we're guessing for months, and even right up until the episode itself, no one will know. That'd be a really fun way of doing it, might be a bit annoying, but fun none the less.
As for villain for regeneration, as much as I love the master and daleks, they've been overused for the regeneration storyline. Although I wouldn't want a new villain to be in the storyline (unless it was a really cool one like the Silence). Hell, maybe use the Silence or eeping Angels in the regeneration storyline.