I was wondering why I never got past the first level, and now I know - like the first game's first level, it's a brutal slog to get through, but this time you don't have an easier second level that you can play to get your strength up first. The second level was, on the other hand, incredibly easy as I crushed the CPU with only three factories built.
The first game had flavor text at the beginning of every level, telling you who you're fighting and why the area is valuable. The lack of that here hurts the storytelling somewhat. The fact that the first cyborg soldiers are unlocked after the second level is completed makes me think that gameplay and story integration isn't near the top of the game's priority list.
Other commenters have complained about bugs - while the are some bugs that are holdovers from the first game, like the game chugging when there's lots of bullets on-screen, I ran into one where the sound of rain would not go away, even when all the in-game sound was turned off. Restarting the game fixed this, but it wiped all my progress, so this is probably as far into the game as I'll get. This might just be a Newgrounds Player thing though.
The core gameplay is still fun, but this game has a lot of things holding it back compared to its predecessor.