Plants seem to be less complex organisms than animals, but despite that there are less plant genomes sequenced. Is that because plant genomes are more complex, for example in terms of regulatory regions and transposons that make sequencing more difficult, or are there other reasons why the number of sequenced plant genomes is smaller than animals?
The authors of this 2012 review article summarize the problem well in their introduction:
In contrast to the tremendous advances in throughput, assembling sequencing reads remains a substantial endeavor, much greater than the sequencing efforts alone would suggest [22-24]. Large complex plant genomes remain a particularly difficult challenge for de novo assembly for a variety of biological, computational and biomolecular reasons. Plant genomes can be nearly 100 times larger  than the currently sequenced bird , fish  or mammalian genomes . In addition they can have much higher ploidy, which is estimated to occur in up to 80% of all plant species , and higher rates of heterozygosity and repeats  than their counterparts in other kingdoms. Furthermore, the gene content in plants can be very complex, as shown by the presence of large gene families and abundant pseudogenes with nearly identical sequences derived from recent whole genome duplication events and transposon activity . Plants tend to have high copy chloroplasts and mitochondria organelles, which complicate assembly of their remnants in the nuclear genome and skew coverage levels . Finally, it is often very difficult to extract large quantities of high-quality DNA from plant material, making it difficult to prepare proper libraries for sequencing.
From: Schatz, Witkowski and McCombie. "Current challenges in de novo plant genome sequencing and assembly". Genome Biology (2012). 13:243
As you can see, all of the key reasons have been touched on by the various people who have commented below your question.