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Answers
From the Linnaean beginning, the principal criterion for the classification of flowering plants was the flower itself — its structure, number of parts, etc. This was, for the most part, a pretty accurate way of classifying flowering plants.However, as years went by, other elements of morphology (form) came to be considered more strongly as well — general plant structure, seed development, vascular bundles, pollen form, etc. Chromosome counts started to be used to help distinguish species and hybrids. Another factor was specialized chemical analysis; for instance, a certain form of enzyme might only be found in closely-related plants. Geographic distribution was of help in the lower levels of classification.
Another critical factor that came into play was paleobotany. Ancestral forms of plants sometimes pointed to modern relationships.
Then they started doing genetic analysis. This mostly started with chloroplast genes. However, there was a problem with this in that it did not always give completely accurate information. In more recent years, more analysis has been done on nuclear gene sequences, which is the most accurate means of classification we’ve ever had and possibly will ever have.
However, ferns had no flowers and could not be so analyzed. The form and shape of the sorus (clusters of sporangia) in a fern was the original principal criterion. The form of dehiscence of the sporangium was recognized as characteristic of larger groups. The spores themselves came to be analyzed for form and structure. Other factors included the general factors cited above for flowering plants, other than the flowers or pollen. Today, genetic analysis is also critically important with the ferns — and the lycophytes, and non-vascular plants, etc.
Leaf or frond form is not a very good criterion for classification except in closely-related groups.