What are some limitations with flywheel resistance training (FRT)? One of the major things I think you need to be aware of is that due to the maximal or near maximal effort and non-stop nature of the of FRT, there is potential to rack up significant fatigue, as you are training closer to failure with each rep.  

This could be viewed as an advantage also as it is believed that final repetitions of each set in traditional resistance training, where effort is near maximal, is where all the magic happens in terms of strength and power adaptation.

Nonetheless, it is acknowledged that the mechanical and metabolic overload is greater in flywheel training and those using it need to be aware of this and structure rest and recovery accordingly.

There are others of course, such as not being able to train isometrically with this technology, the inability to perform some exercises such as the snatch, clean and jerk, as well as plyometric/ballistic type activity. Many of these limitations can be overcome with combination type training e.g. flywheel squat training + explosive jump/plyometric training.