Best I can tell, you're best off focusing on your offense, starting with power, number and frequency of shots (In that order). Upgrade them all to 2, then all to 3. Then you should hit the armor, and by the time you're at the end you should be in a good place to take on the last boss.
This is just what worked for me, YMMV
My bunny seems to get stuck a lot running in a direction, to the point where I just get stuck in a corner for the rest of the level. I really like the concept, but this might be a deal-breaker for me, since it seems to happen every other level.
I rated this one a 5, so suffice it to say, I thought it was overall a great game, but I'd really like to point out the animation. This game has some of the smoothest animation I've found in a flash game. Nice work fellas.
Overall I dug this a lot, although I'd like to see a few more things. I understand it may imbalance the game a bit, but I think a run speed upgrade would be welcome.
Also I'm not sure if it's the layout, but the barricades don't seem to help much. It's not worth making sure they're all repaired. If you just build some turrets and cover the left room's barricades it gets pretty easy.
I'd like to see some more guns too, since I was all maxed out I could just dump cash into turrets and consequently, I barely had to fire a shot on the last level.
Overall I liked this one a lot, but I would have liked a bit more difficulty and some more upgrades.
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