Paper:
System identification of complex and nonlinear systems is a central problem for model predictive control and model-based reinforcement learning. Despite their complexity, such systems can often be approximated well by a set of linear dynamical systems if broken into appropriate subsequences. This mechanism not only helps us find good approximations of dynamics, but also gives us deeper insight into the underlying system. Leveraging Bayesian inference and Variational Autoencoders, we show how to learn a richer and more meaningful state space, e.g. encoding joint constraints and collisions with walls in a maze, from partial and high-dimensional observations. This representation translates into a gain of accuracy of the learned dynamics which we showcase on various simulated tasks.

Review:
Thank you for the detailed reply and for updating the draft 
The authors have added in a sentence about the SLDS-VAE from Johnson et al and I agree that reproducing their results from the open source code is difficult. I think my concerns about similarities have been sufficiently addressed.
My main concerns about the paper still stem from the complexity of the inference procedure. Although the inference section is still a bit dense, I think the restructuring helped quite a bit. I am changing my score to a 6 to reflect the authors' efforts to improve the clarity of the paper. The discussion in the comments has been helpful in better understanding the paper but there is still room for improvement in the paper itself.
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Summary: The authors present an SLDS + neural network observation model for the purpose of fitting complex dynamical systems. They introduce an RNN-based inference procedure and evaluate how well this model fits various systems. (I’ll refer to the paper as SLDVBF for the rest of the review.)
Writing: The paper is well-written and explains its ideas clearly
Major Comments:
There are many similarities between SLDVBF and the SLDS-VAE model in Johnson et al [1] and I think the authors need to address them, or at least properly compare the models and justify their choices:
- The first is that the proposed latent SLDS generative models are very similar: both papers connect an SLDS with a neural network observation model. Johnson et al [1] present a slightly simpler SLDS (with no edges from z_t -> s_{t + 1} or s_t -> x_t) whereas LDVBF uses the “augmented SLDS” from Barber et al. It is unclear what exactly  z_t -> s_{t + 1} is in the LDVBF model, as there is no stated form for p(s_t | s_{t -1}, z_{t - 1}).
- When performing inference, Johnson et al use a recognition network that outputs potentials used for Kalman filtering for z_t and then do conjugate message passing for s_t. I see this as a simpler alternative to the inference algorithm proposed in SLDVBF. SLDVBF proposes relaxing the discrete random variables using Concrete distributions and using LSTMs to output potentials used in computing variational posteriors. There are few additional tricks used, such as having these networks output parameters that gate potentials from other sources. The authors state that this strategy allows reconstruction signal to backpropagate through transitions, but Johnson et al accomplish this (in theory) by backpropagating through the message passing fixed-point iteration itself. I think the authors need to better motivate the use of RNNs over the message-passing ideas presented in Johnson et al.
- Although SLDVBF provides more experiments evaluating the SLDS than Johnson, there is an overlap. Johnson et al successfully simulates dynamics in toy image systems in an image-based ball-bouncing task (in 1d, not 2d). I find that the results from SLDVBF, on their own, are not quite convincing enough to distinguish their methods from those from Johnson et al and a direct comparison is necessary.
Despite these similarities, I think this paper is a step in the right direction, though it needs to far more to differentiate it from Johnson et al. The paper draws on many ideas from recent literature for inference, and incorporating these ideas is a good start. 
Minor Comments:
- Structurally, I found it odd that the authors present the inference algorithm before fully defining the generative model. I think it would be clearer if the authors provided a clear description of the model before describing variational approximations and inference strategies. 
- The authors do not justify setting $\beta = 0.1$ when training the model. Is there a particular reason you need to downweight the KL term as opposed to annealing?
[1] Johnson, Matthew, et al. "Composing graphical models with neural networks for structured representations and fast inference." Advances in neural information processing systems. 2016.