Don't get me wrong, I prefer Nanoha over Tutu mostly because where Nanoha is without a doubt more shallow in terms of plot it makes up for it by being a fast paced anime with a new take on a genre I've never been that attached to. I love the character designs, their attitudes and the neat gimmick they got going with the magic technology, especially in A's.
However, I can't deny that Tutu has a better plot and a fairly good end to it all. It takes longer to get into (depends really, a fair number of people didn't like the first season of Nanoha because it's a bit slower then A's and has a cliche start) but once it's rolling, especially around the half way point it really starts to shine and pull you along. It's main drawback is that it is a lot more like traditional magic girl shows, where I'd be tempted to call Nanoha a shonen, Tutu is more a magic girl show done well.