Hey there folks. After a little bit of time to reflect on the madness that can be the LD Compo, I've thought about my game as a whole and the overall process. If you have the time and inclination, please check it out here! I make it a point to reciprocate ratings and feedback to anyone who's taken the time to help. Only one case so far have I had to forgo reviewing a game, but only because the game doesn't have a build I can run (currently macOS/Web).
And now for something I thought would be much shorter than it actually is.
In the Beginning...
When the final round of voting started I was talking with some friends about potential ideas, and one of them stuck to the "more you have, worse it is" idea. They suggested managing a reactor and keeping it from overloading. I kept the idea in my head and when the theme was selected for LD40 I tried to think of an interesting way to implement the idea. Unfortunately it seemed to me that every idea I had I was either unsure of how to implement or so far beyond my knowledge that attempting to go for it would be an exercise in frustration. I had also talked with the developer of the FES Unity framework, but unfortunately by the time I had the chance to look over the documentation it was too close to go time and I couldn't make use of it.
That "Ah ha" Moment
So 9:00PM EDT rolled around and the compo began. I started thinking of ideas for the reactor concept my friend came up with, and my first thought was something like "Keep Talking and Nobody Explodes" -- on the right side of the screen would be some sort of set of minigames used to lower the power level, and as the power level went up some "needy" distraction elements would come online and threaten to end the player's game. I wasn't able to figure out how I wanted to implement the idea, though, and as the first hour ticked along I was faced with the dilemma to keep hammering at the idea or come up with a new concept. I chose the latter, and it didn't take very long to get an idea I was happy with. What if, instead of a reactor, the thing you had to manage were ores being dumped into bins, and you had to process them to keep them from piling up? And that was the "ah ha" moment. The idea was simple and had enough potential to build off of, so I got started.
Night 1: 9PM to Midnight
After I had the basic idea, the time came to implement it. I created the ore pieces in Aseprite (using a wacom tablet) and managed to make an asset that I thought looked good enough to get started. I then did the same for the bins, and got started coding in the ore falling from the conveyor belts into the bins. By the end of the night the ore moved slowly down the belts, hit the ore bin and was destroyed, adding a point to the bin's counter. This took a good bit of time (which flew by) and before I knew it it was midnight. So I went to bed and woke up the next day ready to continue.
Day 1: 7AM to 5PM
The first day ticked along and I got the mechanics for the boxes filling and overflowing set up. I also got the player and their movement working, complete with slowdown as the boxes overflowed. A few more mechanics (like scoring) and a few more hours later and it was time for me to get ready to go to dinner celebrating a family member's birthday -- something I thought was going to take maybe two hours. As it turned out, though, even with reservations it was nearly a four hour time away... time I thought I scarcely had.
Night 2: 9PM to Midnight
When I returned from the party I immediately set to designing the UI. During that process another idea hit me -- a way to upgrade your bins. I wasn't sure if I could make it work or not but my thought was "Well it's only one gameobject and a few script edits so if things don't go right I can revert easily enough." Thankfully that wasn't necessary, and the upgrade mechanic actually worked fairly well. Midnight rolled around again so I wrapped up and got ready for sleep.
Day 2: 7AM to 9PM
The final day had rolled around, and all that really remained was polishing up the graphics and making sound and music. I set to work on that, cracking open Aseprite (amazing sprite editor, by the way), Bfxr (an evolution of the LD classic sfxr) and Terry Cavanagh's amazing Bosca Ceoil music tool. I hammered out the sound and music, and went on polishing up the graphics to something I'd enjoy looking at. Along the way I thought of revisions and enhancements to the game (such as a combo system and the "information messages" that flash on the screen when you try to perform an invalid action). The day ticked on and I started fixing major bugs around 6PM. I think the final version of the game went up at 8:40PM, after fixing some UI stuff and fussing with Unity's animation system. I worked on the itch.io page and my LD submission, hit the go button and things were done.
Postmortem
What went well
Honestly? A lot more than I thought would go well. The upgrade system is basic but gives the player some breathing room, and adding a combo system to the alloy scoring gives the player an incentive to play risky. Tightening the failure condition from "All boxes overflow to max level" down to "2 boxes overflow to 10 of 12 and 8 seconds pass in this state" really made the game feel much more coherent, and fixed a few potential exploits.
What went badly
I'm not happy with the music. I love the drum beat I created (it really has an industrial feel, in my opinion) but the lead of the song sounds like bad elevator music. Also I'd really like to improve my art skills. Making graphical assets with a major visual impairment is difficult (but doable -- if you haven't played my game yet don't let this influence your votes!) and I know there's room for improvement.
What I learned
The biggest thing? Sprite animation in Unity and some of the difficulty in making an animation tree that has an aspect that forces you into a stop state. I almost scrapped the sweep animation altogether because I couldn't figure out how to make it work.
In closing...
This has been an amazing Ludum Dare, and I feel like I lucked out with a theme I could really push an idea out for. I was a whole lot more relaxed this time than in LD38 (we don't talk about LD39...) and that made so much of a difference that it felt almost easy by comparison. I love the way that Ludum Dare pushes my mind to its extremes then keeps on going. And I have what I personally feel is my best game yet to show for it.
If you've read this wall of text, thank you for taking the time.
This second screenshot shows two of the enemies -- the Bomber by the top-left tower will wander between the towers, placing its little packages of death by your towers. Seconds later and boom, no more tower (though I'll probably balance that down... OHKOs aren't cool.)
The other enemy, trying to hide under the health bar, is a Collider. It picks out the nearest target, either you or a tower, and homes in on it with the intent to ram it. There's one more enemy type I plan on implementing, but I can't show the Shooter if it doesn't shoot yet!
I really wish I had known about coding 
The UI, especially its scaling, proved to be something that I didn't expect to have difficulty with. I apparently didn't set up the RectTransforms up properly for the title screen and status UI, and then went and changed my game's resolution while it was still scaled for a higher resolution (so that people with 720p monitors could still play). I really should have, rather than using the end of the compo participation time to get in early and ensure I didn't get hit by any snags, used that time to more thoroughly test the various builds under the lower resolution. Then maybe instead of having to post a critical 
Another thing that proved to be a problem was my inexperience with Unity. However, as it's the best I have for making games, it was either enter with an incomplete, novice understanding of the engine or not enter at all because I don't feel like GameMaker Studio fits my programming style, and don't feel like RPG Maker MV would have been a suitable engine for a compelling LD entry. My inexperience really is the thing that interfered with my progress the most all throughout the event with documentation look-ups and needing to make tiny iterations on some of the code to get the functionality working properly.
Well, that's my second Ludum Dare down, and it went better than I thought it would, given what I thought would be a 1-hour dinner turned into something that took over three hours. I learned some things about Unity, and overall feel like the time spent went rather well, in no small part to the people participating in my stream.