You'll have to assess which aspects of the plays you are going to compare. Are you going to compare the two main pairs of lovers (Benedick and Beatrice, and Romeo and Juliet)? If so, there is a wealth of things you can say about these two couples.
You could contrast them in age and experience -- Romeo and Juliet are both teenagers experiencing their first real romance. Romeo may have had a thing for Rosaline before, but Juliet is the only true love he's had so far. Romeo and Juliet are very inexperienced lovers, and some of that naivete contributes to their disastrous end.
Benedick and Beatrice are adults, by comparison, and have had experience of each other before ("I know you of old" says Beatrice, I.i.) They are much more of an age to understand themselves and the perils of any romance. (Leaving aside the fact that Romeo is a tragedy and Much Ado is a comedy, which of course makes the ending in each play very different, the composition of the characters does contribute to the differing endings).
It might be interesting to compare the verbal sparring that goes on between the two couples. Romeo and Juliet do a little verbal gameplaying (at the Capulet party) but it is mostly gentle, and with the clear idea of marriage in mind. Romeo is smitten with Juliet, and she with him. There isn't really any suspense whether or not they will fall in love -- it becomes quiet clear very quickly.
However, Benedick and Beatrice fight their attraction mightily. They make a huge show of disliking each other in public, while they admit their love for each other only to themselves ("By this day, she's a fair lady" says Benedick, II.iii). Everyone around them knows that they are in love with each other -- and conspire to get them together.
Romeo and Juliet, however, by necessity hide their love from all but their closest confidants (the Nurse, Mercutio) and no one around them (certainly not their parents!) think that they would be a good match. While everyone and everyting conspires to get Benedick and Beatrice together, nothing helps Romeo and Juliet -- and events (the lost letter, for example) cause them to be pushed apart.
In essence, Benedick and Beatrice are meant to be, and Romeo and Juliet were not. You can look on it as pure chance, or, perhaps, as Shakespeare might have looked at it, the effects of fate or the stars or the will of the people around the lovers which has such a great control over what happens. I think a thesis statement combining one or more of these ideas of the couples' differences might be an interesting and effective beginning to your paper.