It is common for laypersons to get extremely excited about the possibilities of induced polyploids in plants, especially ornamental plants. Many think of the chemicals used to induce polyploidy as a "magic sauce", and attempt to use them carelessly, and in so doing, put themselves at significant risk. Polyploid induction chemicals can be extremely dangerous to use!
But even when done properly, safely and with appropriate caution, there are frequently problems --- true horticultural problems --- with induced polyploid plants.
Delayed germination: It is extremely common for seed germination in induced polyploids to be delayed when compared to the parental diploid lines. This can be true for many generations following conversion, although time-to-germination is generally a selectable trait. For example, diploid Pelargoniums typically take 5 to 7 days to germinate, while tetraploid pels typically take 10 to 12 days.
Delayed flowering: Induced polyploids frequently take longer to come into flower than comparable diploid lines. This can be an advantage if slower flowering (i.e., non- or late-bolting) is desirable, but for flowering ornamentals, this delay would generally be perceived as a flaw.
Slower growth: Induced polyploids invariably grow slowly in the first generation, the generation which was converted. However, slower-than-diploid growth rates are not at all uncommon in induced polyploids, regardless of how many generations have passed post-conversion. This is not a universal characteristic of induced polyploids, but it is quite common. This slower growth rate is likely to be the same effect that one observes when the induced polyploid is considered to be more compact or more stocky than the diploid.
Decreased cutting or seed yield: Another potential drawback with induced polyploids which is also likely related to a slower growth rate is that polyploids frequently have decreased seed yields (fewer but larger seeds), or decreased cutting yields (slower growth rates lead to slower production of cuttings). As a breeder, you want your developments --- your products --- to be produced and sold in high volumes. As such, your products need to be produce-able.
Decreased flower production: One of the benefits of induced polyploids is larger flowers. The flip-side of larger flowers is that larger flowers in polyploids may have a cost: fewer flowers. As an ornamental breeder, you frequently want BIG flowers, but BIG must always be balanced by flower number. Selecting for total floral display may cause you to select away from the largest flowers possible.
Changed plant architecture (more coarse, less refined): Polyploids frequently have a distinctly different plant architecture than the comparable diploids. Polyploids can appear to be coarse, open, and less refined. However, this can also be viewed as an advantage, especially if the less-refined habit provides a better display for larger flowers. Bigger leaves, thicker leaves, reduced branching --- all of these structural changes may create very different plant architectures with induced polyploids. That said, leaf size and branching are highly selectable characteristics, whether at the diploid or tetraploid levels. You can breed tetraploids to have the more refined tetraploid appearance.
More vigorous growth: Induced tetraploids may also demonstrate more vigorous growth than comparable diploids. Again, this becomes a matter of trial-and-error. And again, if more vigorous growth occurs, it is generally not in the generation which was converted, but in future generations.
On the left (below) is a tetraploid Bacopa seedling. On the right is a diploid seedling (Pan American's Snowtopia). Please be aware that increased vigor like this does not always occur with induced polyploids.
And no, the tetraploid seedling on the left has not yet flowered. It may have large flowers; it may not. Not all tetraploid bacopas have large flowers.
Larger leaves: Many induced polyploids have larger leaves than their comparable diploids. You can see this in the bacopas in the image to the left. This may or not be beneficial. However, large foliage can often appear "cabbage-y" and this is not generally considered to be a positive if you are not breeding vegetables.
Genetic junk: Last, one of the important considerations to remember is that when you induce polyploidy, you create more opportunities for things to go wrong during cell division and during gamete production. Slow growth rates, reduced fertility or fecundity --- these may simply be reflections of chromosomal pairing abnormalities because there are extra sets of chromosomes in the dividing cells. For this reason, as a breeder you should probably go through at least two seed generations post-conversion before making final selections. You may find that what may have been potential problems simply disappear. More, the new combinations of alleles that you are hoping for will ONLY occur in the advanced generations, as recombination begins to work for you, and the genetic debris from the initial conversion gets sifted out by meiosis.