Both zhan zhuang and neidan are legitimate practices of chi. The former is the foundation practice of all internal martial arts. The current form that people practice is mainly influenced or developed from I-style Grandmaster Wang Xianzhai (王薌齋). Primarily it aims at building a sound body structure fit for combat. Because of its relation to chi, the basic forms of which have also been widely used for health and "longevity" purpose (養生). Today it has become a very popular practice in the East. Its benefits for both body structural building and health enhancement have generally been accepted and many people got good results.
Scholars can refer to old literature to show the prevalent of this practice in ancient China. And as far as having a long history it is the same with another important practice: Neidan , some refer to it as Taoist yoga or Taoist meditation. For more technical discussion in which more precision in terminology is required, the use of the word Neidan is to be preferred.
In the East, the most common practice of Neidan is developed from the Dragon Gate (龍門) branch (from Taoist Qiu Chuji 邱處機). One major reason is because of the popularity of the text 性命法诀明指 (translated into English as Taoist yoga by Charles Luk) by Master Zhao Bichen as well as the popularity of the text 慧命經 (Hui Ming Jing translated in English by Richard Wilhelm, an extract was included in his translation of The secret of the Golden Flower) by Master Liu Huayang (柳華陽). Many masters of today claimed to be direct lineage from the Dragon Gate branch, including Taoist master Wang Liping (王力平) in Mainland China who wrote a text called 大道行 (The way of Dharma) on his mythical initiation procedure from a very young age.
Nowadays, however, few people practice Neidan. And many who claim they are doing fail to understand even the first stage of the practice: microcosmic circulation.
The obstacle of Neidan's popularity is its mythical character. The proclaimed objective of any Neidan practice is to become an Immortal. Without a proper understand of the theory behind, one may easily misunderstand Neidan as some kind of secret cult with potentially harmful side-effects (I have written a previous post explaining the theory behind the objective of becoming an Immortal.)
Apart from the Immortality issue, books on Neidan are famous for their many obscurities, metaphors, and sometimes contradicting assertions between the texts. I, however, don't see the obstacle as its hindrance, because masters of later dynasties, like Zhao Bichen had already simplified their approach. The problem is many "practitioners" falsely believe the existence "profound hidden meaning" (ultimately taught or reviewed by some higher-powers) in the old texts, notably Can Tong Qi (參同契). And I personally know some who believe if they can truly decipher the hidden meaning inside these ancient texts, they will "miraculously" achieve the highest level of Immortality! And these people spent many of their precious hours doing this kind of futile search, instead of using existing knowledge, sit down, meditate, read, think and improve.
Another obstacle is, mainly in the west, some practitioners claimed that the requirement of the initial stage of microcosmic circulation doesn't work. Or, the sublimation of sexual energy doesn't work. Based on this faulty understanding, some of them follow certain masters in the West and buy into sexual chi-kung proper. That unfortunately will be another cup of tea, and a cup of tea condemned by major Taoist masters.
A related obstacle is that practitioners fail to understand the intricacies of the sublimation process and/or fail to do the preliminary foundation that will be required to do a successful sublimation. For readers who are interested to understand and learn can refer to my previous post: The secret Taoist concept of the right moment.
Here I end my first comparison. Conclusion: one simple, one (looks) complex.