At the start you still believe you're the hero. It's a good point though. I'd say more about the resolution but spoilers.
Maybe the fix would have been simple. As soon as you start eating out of dumpsters or stealing the people should have run in horror, realising that you are the one. Or even just when you enter an area brandishing a gun.
For the enemies I sort of suspect they just went out of scope (or passion?) and didn't add more types.
There were lots of versions of 'guy with a gun' but that's not very interesting. The game would have been a lot more entertaining if it had featured more steampunk style enemies - robots, guys in loading suits, guys flying with gyro copters etc. any reasonable image search on deviant art would produce more engaging enemy designs. The handyman was cool, but yeah he should have reacted to being hit in the red ball. Was that even a weak point? The patriots as well I just bombed.
Instead we got the same enemies from bioshock1. I was confused by the firemen and crow guys. The turret was especially disappointing. It felt like going to a restaurant (slightly cheaper) and being served reheated leavings.
The story and it's presentation is excellent though. I don't play many AAA games so maybe I'm blinkered, but I can't think of a better story in another game.
On that note, here's a bioshock 1 thing...
http://www.pentadact.com/2009-04-15-ending-bioshock/