As much as I enjoy this game, I must point out that the tutorials tend to be near worthless, as it's very easy to do levels out of order, and end up getting acquainted with a new obstacle well before you are ever given a hint on how to use it.
I think as soon as you bring the grain, the village needs to start growing within a year, to indicate that you've done something correctly. With the trees and the water, they grow and change quickly enough that I know that I'm doing something right. But with the village, it takes much longer. I'm too afraid to burn that many years on what might be the wrong solution, so after seeing no change for a couple years, I'll wander around some more and look for something I might have missed, checking each season one by one. After about 15 minutes of checking the entire explorable area in each season, I'll notice that something seems kind of different about the village, and only then realize that I'd solved the puzzle all along.
Ivod's suggestions are good, but I highly recommend you buy one Emergency Device among your accessories. When you enter secondary fire with one equipped, all bullets near your ship will turn into harmless coins, allowing you to escape sticky situations. However, after you use it, you have to wait something like 5-10 seconds to use it again.
One of the comments mentioned that in ancient Roman times, thumbs up meant "kill" and thumbs down meant "don't kill". To that end, I think you should add an option at the start of the game, between Classic mode and "Historically Accurate" mode. (Classic mode changes nothing, "H.A." mode just reverses what thumbs-up and thumbs-down do, except for at the elevator and the statue.)
Skullface, he's got a big skull face! He's got the body of a skull, and the face of a skull! And he flies through the air, cause he's got a skull face! Skull face!
I have a few suggestions on how to make these completely separate game mechanics more integrated with each other. First, make it so that the Pong ball is your primary method of attack. Make the waves so ridiculously large and fast that it would be impossible to take them down with an ordinary gun, thus justifying the use of this giant energy ball which can steamroll through enemies effortlessly. And second, get rid of the shield, and replace it with a gun that shoots paddle-sized ammo, which you can use to bounce the ball and destroy enemies (but make sure to limit the gun's rate of fire so that it's not as destructive as the ball).
Well, it's an interesting concept... but unfortunately, rather than feeling like a fusion of two games, it just feels like you're playing two completely separate games at once. The Pong ball just passes through the Invaders harmlessly, so I'm just left questioning why you're even bouncing this ball around in the first place. Plus, having to constantly hold down a key to keep your bouncer shield on gets rather tiring.
xzxzccc: The main character is always called a protagonist, and the one who opposes the protagonist is an antagonist. The two movies you listed are examples of Villain Protagonists.
 "Super Duck Punch!"){kind=icon}
 "Decision 2"){kind=icon}
 "Turnament"){kind=icon}
 "Give Up"){kind=icon}
 "Hello Worlds!"){kind=icon}
 "Code Fred: Survival Mode"){kind=icon}
 "Beloved"){kind=tracking}
 "Infectonator : World Dominator"){kind=icon}
 "400 Years"){kind=icon}
 "Frantic 3"){kind=icon}
 "Robot Wants Fishy"){kind=icon}
 "Caesar's Day Off"){kind=icon}
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 "SkullFace"){kind=icon}
 "P*NG INVADERS"){kind=icon}
 "Squidy 2"){kind=icon}
 "Fractured"){kind=icon}
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I'm not even sure how such a mechanic would work in 3D.