I prefer 2D/traditional animation. If its 3D then it has to be Advent Children quality. The best is the mix of the two. You don't see much anime these day with traditional animation where everything is hand drawn. The only 'modern' anime I can think of that was all done by hand is Scryed.
The bad thing about 3D is, it is hard to imitate human movement naturally. So we always end up seeing unnatural movement of characters in a fully CGed anime and sometimes the voice doesn't match the lip movement of the character. Another con is, it is too time consuming and costly to make it. Look at FF7 AC, it took them 4yrs to make a 101 minute movie which is about an hour or so long.