Moxie's criticism of portknocking implementations [1] has several facets that apply to fwknop. I would not recommend using fwknop in general.
Unrelated to security, but practical experience from using fwknop in the past: port-knocking tools that depend on timestamped packets are a great way to get locked out of your server if you have time skew between server and client. EC2 instances will drift a lot over their lifetime, so if you're not running NTP you will likely eventually fall outside the portknocking implementation's grace period, and then be unable to access your server at all, short of rebooting it or figuring out how skewed the clock is. Not fun.
First, let me state that I have a lot of respect for Moxie. That out of the way, knockknock is not above criticism too:
1) It is possible to mount a MITM attack against knockknock just by intercepting a knockknock packet, changing the source IP, and retransmitting. This is a consequence of knockknock not encrypting the source IP within any payload (which involve only packet headers in the knockknock implementation). fwknop does not suffer from this problem because it encrypts the IP to be allowed within the SPA payload.
2) You mention time synchronization issues above. Well, knockknock uses AES in CTR mode, and this also requires synchronization between the client and server of a different kind. If synchronization were a problem for fwknop, then you must apply this critique to knockknock too.
You _can_ disable time sync in fwknop if you really want to, but it was added to prevent MITM attacks.
Here are the design goals that fwknop is developed around:
I agree that there are certainly a number of tradeoffs involved, and reading the design goals you linked, I see that (in particular) the desire to be able to run fwknop on OpenWRT and other particularly resource-constrained setups makes a strong argument for your implementation strategy.
Your comments on MITM and synchronization are well-received. It's clear that you take the security of the fwknop implementation seriously, and I apologize if I was overly negative. I should have read more about the design goals before criticizing the project so harshly.
For what it's worth, in place of my first comment, I should probably instead say that fwknop was not a good fit for my needs at the time, but that there certainly exist cases where it will be an excellent solution, and to watch out for a practical gotcha I learned the hard way. :)
Unrelated to security, but practical experience from using fwknop in the past: port-knocking tools that depend on timestamped packets are a great way to get locked out of your server if you have time skew between server and client. EC2 instances will drift a lot over their lifetime, so if you're not running NTP you will likely eventually fall outside the portknocking implementation's grace period, and then be unable to access your server at all, short of rebooting it or figuring out how skewed the clock is. Not fun.
[1] http://www.thoughtcrime.org/software/knockknock/