It seems a lot of the arguments around e92 or e93 focus around the e93 not being a "real" M3, because of the extra weight, less rigidity, etc. I think that's BS, but fine, let's say it's accurate.
So what? Simply decide if you want a really fast convertible, or a really fast coupe. You'll be able to feel the difference only under very specific circumstances (e.g. track), and even then most people probably can't.
So I'd say choose the e93 (and I did
) because it's a coupe - and then the top comes down.
In answer to some of your key questions:
The trunk is definitely on the small side, but so far the only thing I can't fit has been a bike frame. About $200 in groceries fits just fine with some care (with the top up).
Mechanically they're under the same warranty. Assuming you have access to a BMW dealer, service issues shouldn't be a problem. I've had a problem with my top, so it's possible that they do go out of adjustment eventually - others should also speak up tho.
And finally, who cares if people can see you? Wind in the hair while driving is fantastic, the top has been down on mine more than it's been up.
Both are great cars, you'll be in good shape either way.