My take on the MC21 v 28 is that the 21 is the way forward.
As has already been mentioned, it's easier to get power out of and also costs far less to do so.
As for handling, my chosen weapon would be the 21. Having ridden both back to back with very similar engines and suspension, I consistently lapped quicker on the 21 and felt it had more stability than the 28.
Possibly two reasons. The first and most fundamental would be the swingarm. The Pro-Arm by Honda's own admission has "passive steering" which in layman's terms means it bends like a banana when stressed. The normal type 21 arm doesn't do this and as such gives more confidence and can be pushed harder in my opinion. The RS250 suffered these same symptoms and Honda knew it but refused to take (what they considered) a step back.
There's also the fact that the 28 has a huge hole in the headstock for the steering lock. The 21 doesn't. My engineering background says that this will be a weak point. Honda recognised this by suppling a bolt in piece for racing, but it doesn't really help that much. And when you consider that the F3 frame has a massive headstock then this is definitely an area that you don't want to have big holes in.
However. I tend to look at these things from a racer's point of view. So what about you're road going guy?
Well, the Pro-Arm will attract attention as it's obviously a little special and the MC28 does have sexier bodywork (just my opinion). Also the key card is just so trick, even though it serves no real purpose other than making it expensive to derestrict. But it does look pretty cool when all others have bunches of keys and you have a card.
So, what would I have? Well that's easy cos I've been there. It'd be a 21 with 28 bodywork. Hunt for an F3 shock to prop up the rear and either RWU NF5 or USD NX5 forks. That would give you an almost unbeatable package through the twisties on a Sunday morning hoon.