honestly speaking, i think that the manga is the best (it covers so much beyond any animated bit)
that said each of the animes has its own strengths and weaknesses.
Mahou Sensei Negima:
It was Truer to the plot, not that it was that hard. and the battle bits were great in the negima sort of way
The original anime had a fairly cruddy animation style, and left out a lot of the plot*cough*Kotaro*cough*
and i'm so not even going into the ending of it....not to mention i think it did a bad job of getting each of the characters, well, characteristics right. all in all it wasnt as bad as it could have been but close
the Second was far better animated, and i think it covers the characters characteristics better. It does a lot better job on many fronts.
Only two things really.. The first was the plot. just who's ass did they pull it from? The other was the pactio system in it.. Suka cards....i enjoyed it more than the first but it kinda felt like another anime with a negima skin(yea thats harsh)
Really speaking though the only one i think that got plot, character design and animation and character characteristics is the Ala Alba Ova. it is just awesome. i know what they said, but i think they should make a third series anyways. styles after Ala Alba. i would so buy that. the Ken+Shaft combination is astounding.
thats my random two cents.