Not knowing is the product
Most people who bounce off NGU Idle bounce off in the first hour, and they are not wrong about anything. It is ugly, every menu is a joke, and it hands you energy, magic, NGU upgrades, Augments, Wandoos, the Time Machine and Blood Magic without saying which of them deserves your resources this hour. Nothing in it is difficult in isolation. The difficulty is entirely that the game will not tell you where to point.
If you liked it, that is what you liked, and it means the usual recommendations aim at the wrong target. The question here is not which games are big, or long, or free. It is which games are deliberately under explained: which ones hand you a system with hidden interactions and expect you to work out its shape yourself, with a notes file open and a plan you revise every few days. That rules out a lot of excellent games, which is the useful part of the question, because most of the genre's best titles are exceptionally well taught.
What NGU is doing, so we can measure against it
Two structures do the work. Rebirth clears your zone progress and your accumulated energy and magic while keeping permanent upgrade levels and your best gear, so it is a rerun at higher speed rather than a loss, and the skill is knowing when a run has stopped paying. Above that sit difficulty modes, Normal then Evil then Sadistic, each rebuilding systems you already understood with harsher numbers and new mechanics attached. Learning the game twice more is the content.
The other half is not idle at all. Adventure mode is a side scrolling fight where bosses are beaten by cycling attack, block, parry, pierce and heal in the right order, and it is where the gear you want comes from. Titans keep working while you are away, but no items drop offline, which is a fair summary of the game's attitude.
One practicality. The live version is the free Steam release from 1 October 2019, Windows only, with cloud saves. The old browser build on Armor Games still loads, but the developer said in July 2019 that he was done updating it and its newest changelog entry is from May 2019, so there is no current way to play it in a tab and no phone version at all.
Trimps
Trimps is the browser answer and it is the closest match on this page. It is free, GPLv2, and it explains nothing. You breed creatures who are both your workforce and your army, push into zones until you cannot out damage what is in front of you, and then portal. Four reset layers stack on that, and Universe 2 is effectively a second game with its own currency living inside your save.
It belongs here rather than on a list of merely deep games because of the failure mode. You hit a wall and the game does not tell you why. One of eight interlocking systems is lagging and finding it is the actual play. Every number on screen is clickable and opens a breakdown of where it came from, which is the game quietly admitting what it wants from you. It idles well, calculating offline progress on return with a setting for how it is applied. It is desktop only, since the page ships no viewport tag and no breakpoint below 1000 pixels, so a phone shrinks the interface to nothing. The free Steam build is the same game in a window.
The honest gap is tone. Trimps is bleak and quiet where NGU is loud and stupid, and there is no gear grind of the kind Adventure mode gives you.
Synergism
Synergism by Platonic is the one to take if the part you enjoyed was auditing your own resources. Five reset layers, MIT licensed, free in a browser and also on Steam, with real offline progress that itemises what accumulated while you were away, up to a bankable cap.
It qualifies on opacity for a specific reason: corruptions. You choose to make a run harder in named ways for a better payout, and working out which combination your build survives is experimental rather than documented, on screens dense with rates and multipliers you hold in your head at once. Know going in that it sells PseudoCoin upgrades which are not cosmetic, raising cube and offering multipliers and extending the offline cap, so numbers other players quote may be running on a paid multiplier. The game is complete without spending.
Idling to Rule the Gods
Ryu82's Idling to Rule the Gods is the deep cut, and its own Steam page does the work for me: the developer writes that it "might also not be as easy to understand as some other games" and points new players at the Discord. That is the NGU relationship with a player, stated openly. It is free, released on Steam on 27 May 2016 for Windows, macOS and Linux, with an older browser version on Kongregate and an Android build, and it progresses while you are offline.
You send shadow clones out to train and fight while you absorb what they earn, and it stacks pets, monuments and god fights on top. It is text heavy and years deep. Take it as the answer to what will absorb the same amount of your life in a form you have to reverse engineer.
Two that are opaque about something else
Kittens Game is genuinely hard to read and it is hard in a different direction. Its pressure is scarcity rather than allocation: a game year runs about thirteen minutes, catnip collapses in winter, every kitten eats, and a village grown too fast in autumn starves. You are not hunting a hidden multiplier, you are being punished for optimism. Free in the browser, paid on Steam and iOS, and its licence forbids anyone else hosting it.
Evolve Idle is the surprise near miss. It has more resets than NGU does, a menu of them from Mutual Assured Destruction through Bioseed, Black Hole and Ascension, each with its own currency, plus around sixty species whose traits reshape your economy for days. It also ships a good built in wiki, reachable from the interface, which explains the reset routes. That single feature is the difference: Evolve wants you to plan, NGU wants you to guess.
The well taught games everybody will recommend anyway
Antimatter Dimensions is the standard answer to every question in this genre and it is the wrong answer to this one. It is the most legible deep game we know: each layer is introduced deliberately, the interactions are stated, and it ends in an automation system where you write your own reset conditions in a small scripting language. Two hundred and fifty hours of clarity. Wonderful, and the opposite of what you asked for.
Melvor Idle has twenty four skills, no prestige reset and no hidden mechanics worth naming, at $9.99 on Steam. Clicker Heroes has one clean reset loop with published formulas and a late game that leans on a ruby shop. Both are recommended to NGU players constantly, and both are transparent games. That is a compliment to them and a mismatch for you.
Where to start
Trimps, tonight, in a browser, free, and do not read a guide for the first few hours. Synergism if you would rather the confusion were arithmetical than military. Idling to Rule the Gods when you want another one nobody has explained either.