Seed Plant Phylogeny

You may be surprised to find out that the relationship between the angiosperms and the gymnosperm groups is still subject to much debate. One of the perennial questions is the position of the gnetophytes.

 One of the reasons for this debate is that the Gnetophytes (one of the gymnosperm taxa we discussed) show several features that are typically associated with the angiosperms, including double fertilisation and vessel elements in their vascular tissue. Do these indicate a close relationship and that the gnetophytes are a sister taxa to the angiosperms or are they the results of parallel evolution?

Wikipedia actually has a nice clear discussion of the alternative hypotheses or for a meatier discussion there's this paper from 2009 in the American Journal of Botany:
Phylogenetic relationships among seed plants: Persistent questions and the limits of molecular data