I have two pithy thoughts here: the last modified dates for most of these files (mostly 2015-2019) are sad to look at, and it's an interesting pack that mostly reviews itself. The detailed readme gives sonicnathan's thoughts on all these levels individually, written years after they were made, in enough detail that I don't really think I need to do the same. I'll give some general thoughts but I'm not going to touch on every level one at a time, other reviewers may definitely want to though, there's a lot of variation here.
The earlier non-story levels, with the Colon tileset, do some interesting things with frogs and queens and so on, but they're mostly linear left-to-right single player experiences. They have a lot of block tiles, often the wrong ones, because Colon (like most official tilesets) doesn't have dedicated tiles for trigger scenery, and no one in 2015 would seriously entertain the idea of a ColonButWithTriggerScenery.j2t. That's an early way the episode shows its age, technologically speaking. Later there's a warning telling players not to save in a level because it's too big, which is no longer an issue, and the Bees event is used for wall/ceiling spikes, and stuff like that. It's all perfectly playable but one does occasionally remember that some problems have been solved in the last 5-10 years. The readme calls some of this out too, including a couple sequences where you need to shoot empty air to make small platforms appear, which gets you stuck if you happened to be inside the platform at the time.
The shooting-empty-air sequences are a great segue into one of this episode's main design principles, what I tend to think of as "mind reading" design, in that you have to be able to read sonicnathan's mind—or, realistically, just shoot and stomp every surface—in order to progress sometimes. There are a lot of things that would count as obscure secrets in other contexts but here are mandatory. What bothers me about these areas is how large they are, you're not just checking each wall in a room, you're wandering the entire level (that you've unlocked so far). One particular example: in the Ship Wreck, there's a one-tile-wide invisible hole in the ceiling. Initially it's walled off by a trigger scenery tile (which looks like a speed block), so if you see that and take note of it and remember which part of the ceiling it was at, you're good! Otherwise you're in trouble. Sometimes help strings or arrow signs will clue you in when you need to stomp a bit of floor, sometimes they won't. There are several more-or-less blind mazes scattered through the pack as well.
A random thought: for all that this is a single player episode, these elements remind me of something like Cracco World of Coins, or the UR Orbs levels. There, some of the progression is equally arcane, but because many players are exploring the same area at once, they can use chat to share discoveries and get everyone to the finish faster. Here you're more on their own. Also, because checkpoints don't do a good job of saving trigger scenery states, often the pack will make you spend many minutes in a row tracking down secret after secret, all the while dodging enemies and spikes, knowing that death will reset all your progress.
That's the negative. Even when the levels do give you hints, like saying a 'lower door' has opened, the hints are often hard to follow. As the pack progresses, linearity gives way to opaque confusion, the platformer equivalent of pixel hunting in adventure games. It's a distinct level design style for sure, it's clearly very intentional, it's part of the grand tradition of taking JJ2 levels in different directions than the official levels intended… it just kind of wears on me personally. I think without the checkpoint problem, and with slightly smaller areas to explore, I'd be fine, I'd regain the thrill of discovery and exploration, but there's just a little bit too much stacked against it right now, especially in the Top Secret level.
The positive is that there is still cool stuff in here! I'm naturally biased, but the Crysilis level is really pretty! There are so many different eyecandy elements thrown all over the level, and yet it rarely feels unapproachable. Yes, it can be hard to keep track of where you need to go next, but there's inventive design and cool platforming sequences! The background is surprisingly detailed for Crysilis too, and the number of enemies seem generally well matched to the ammo.
The readme mentions inspiration from EvilMike's episodes, and this is particularly obvious in the intro/outro text, but also in the use of specific weapons to gate progress, like descending through the level to find a single toaster pickup to blast through some toaster blocks. This is still rare enough to feel cool, I think! It does have the issue where you'll get only 3 or 6 rounds of a weapon, and need to spend every single one of them on the blocks, and definitely not slip up and kill an enemy instead—but in general the ammo and the blocks are close enough together that people probably won't make mistakes.
The readme isn't kind to the Chemical Labs level toward the end, which is mostly storytelling instead of gameplay, but I like it… it's a good example of level design as storytelling, working together with the more traditional text strings. (Levels in general are laid out differently from each other, befitting their tilesets and their story roles.) And then there's a kinda cutscene level afterwards that feels like an Another Story throwback.
For all that the more opaque puzzle solving didn't fully land for me, again, there's other good experimentation going on, like the queens early on. It's that skill of looking at what an event does and thinking about how it could be used, which can be different from how it was supposed to be used. The boss battles do a lot of this too, using flailerangs as added sources of danger, like the monks from Time Tripping. And there's a lot more pepper spray here than in most custom levels, acknowledging that it can be used as a sort of blaster powerup with finite ammo, good against tuf turtles (but also dragonflies).
I don't have much to comment on about the story, though it's neat that the readme goes into detail about what episodes 3 and 4 might have covered. Some of the asides are neat, like the hologram sequence. In general, Jazz is being a hero and Devan is being evil and has lots of evil plans and resources. It suffers from the same problem as a lot of similarly-plotted episodes in that Devan himself is mostly absent, you just get a disembodied voice from time to time, threatening evil against you.
Overall, this is definitely an episode with highs and lows, and I'm having trouble condensing all that into a rating, a number. It's a custom episode in the grand history of many custom episodes, a struggle between good and evil, a classic that we almost never got to see. It's a tour through complex layouts in varied locales, with puzzles to solve and enemies to kill (though that's rarely the focus). It runs a full gamut between basic linear design and whatever the opposite of that is, and therefore, no matter what your favorite point on that scale is, at some point in this pack you're going to encounter areas that are NOT that.