Do you think we will hear something about Retro's secret game?
Absolutely no idea. I'd like to hear about it. But I also wanted to hear about it last year. And the year before that.
It'll have been nearly three years since DKCR was finished, shipped, and available for purchase when E3 2013 rolls around. Retro has had some studio problems between then and now, but they really should be due for a reveal.
I'm not sure if Nintendo wants to go head-on with PS4 and Durango as far as new announcements go. Might be better to show at least some stuff when others aren't. But then it would of course mean a boring conference again.
I think they can, but focus on typical Nintendo stuff. We already know they exist, anyway. I've said it in other threads, but I don't expect much in the ways of truly new, big announcements, but instead reveals of already announced games.
IF all these were to be at E3 2013 IN A DECENT playing form it would be a great E3 for Nintendo. However this is Nintendo we're talking about! Unpredictability defined. I expect to be completely overwhelmed or completely disappointed. No middle ground!
Unless plans have changed all of those should show up. The Mario/Kart/Smash trio isn't a should, but a confirmed. Iwata explicitly said they'd be there, and both Mario and Kart will be playable.
I'd be surprised, and disappointed, if Bayonetta 2 didn't come out in full force. But as you said, this is Nintendo.
Whatever Retro is working on should be a given as well, and Iwata said in January that they had several more co-productions in the pipeline that would be revealed in the coming months, so I expect so see at least one of those.
This too is true.
SMT x Fire Emblem is probably iffy. That game can easily appear anywhere - Nintendo Directs, E3, even TGS despite Nintendo historically never going (considering this appears to be an Atlus production). Hell, maybe it even gets dropped in to Famitsu one week.
As is this. I don't put much value on SMT x Fire Emblem, since I feel it's a Japanese centric game, and much more likely to be revealed to the Japanese press first.