The MC21 is like 6 Kg lighter than the MC28 - I can poo more than that (well...maybe not!).
The MC28 Single side swinger looks the bollox.
The MC28 credit card ignition is just trick and makes the bike all the more exclusive.
Not sure why the 21 is faster, that would surely depend on who is riding it and what the state of tune is (see you at Donnington CheekyMonkey
friendly fighting talk 
) - I thought the stock engines were the same ?
I've not had my MC28SP long but it is the absolute dogs, mine wasn't cheap - £3,000 eeeeek, but it is a genuine, mint, original Repsol MC28SP (1 of only ~1000 bikes) with only 11,000 Kms on the clock.
I think MC21 or MC28 is down to personal choice, mainly regarding the preferred rear end, but as RC46 said - the MC28 is the later model and so may be more desirable to the average prosopective owner.