Alpha upgrade 2 is pretty unbalanced and basically just ties EP to a time gate per expansion. Your Energy and Electricity gains slow to a crawl long before it's worthwhile to Expand again, since every time you double your run time, you get 32x EP. This basically forces each expansion to be about 2 hours, since your Energy and Electricity gain are far too low for the final Alpha/Gamma multipliers to increase EP gain by a remotely comparable amount, reducing gameplay to simply waiting. I get that this is an idle game, but it feels really bad when progression is reduced to (seconds/5)^5 and any progression with the other currencies is negligible. I hope I'm making sense, but it should be pretty apparent that nothing ends up mattering for progression as much as just waiting for a specific amount of time regardless of the other currencies.
I'd highly recommend resizing the game window to fit in the standard Kongregate game frame - I'd suspect that's the main reason your current rating isn't at least 3 stars. In an HTML/JS based game, it should be relatively simple and I think this will help improve player count. Also, the early game pacing is pretty strange. You start off going only slightly too slow at 30sec to a couple minutes, as another user noted. Not quite fast enough to play active, but going idle ends up being unrewarding. Suddenly, the game kicks up to a pace where you're forced to play active by constantly prestiging for the first few EP and going idle effectively gives no progress. It also feels like the rapid pacing spike makes the number of generators a bit excessive, since you just blast through 6-8 without them being any meaningful milestone.
Good job so far, but there's definitely room for improvement
In a game that is supposed to be about "careful planning", you need to update the tooltips to be correct. Walls give +500 food production, not +20. This makes the game seem so ridiculously slow that it isn't worth playing, unless you just happen to discover what the actual rates are. As numerous others have said, you have plenty of room on the screen to add something as simple as "wood production" and the names of the currency used rather than a $$$ dollar sign of (most of the time) a different color that you have to hover over to reveal. If you're going to tout your game as one that "rewards the patient", your first and foremost objective should be to accurately provide information for players. I would be more constructive since these are fixable problems to a promising start, but you seem to have abandoned the project and I'm concerned that these egregious bad design choices may go overlooked rather than improved upon.
A neat idea, but "instructions on the menu" isn't particularly helpful when there doesn't seem to be a way to get back to the menu. A very interesting idea and I hope you continue working on this, but I think its biggest problem currently is not communicating information to the player effectively. A simple option to open up a "help" screen would be incredibly useful. If I'm missing something obvious let me know
Hit a pretty hard wall around e70 money where my skills are optimized but I can't purchase any upgrades even after burning all cooldowns. I guess I just have to leave the game idle for several hours to let the multipliers add up but prestiging now gives a negligible boost and I can't see this being solved unless I can somehow make it to e75 money.
After hitting that, I can't imagine there's much left to the game. The remaining skills are borderline useless ("On prestige" skills aren't particularly useful...) so it doesn't feel like there's anything left to work towards.
Prestige only works with gold per second, which is completely useless because you have to click to gain any actual profit. Also, there feels like there is no need for the cost of housing to jump exponentially based on the number of houses already present. The gold per second gain from having more buildings is so tiny that paying 1mil+ for a single well later on is beyond worthless. The balance overall needs to be adjusted quite a bit as the price scaling is nowhere near in line with the gold output. I understand this is an incremental game but the time required for a payout basically requires the use of an autoclicker since idling will virtually never pay out late game.
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 "Ability Clicker"){kind=icon}
 "Miner"){kind=icon}
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