I gave it another spin! I like the new obstacle variety, and the speed boost is definitely a plus. Your updates are a big step in the right direction!
It still gets a little monotonous after a bit though. Part of the problem is that as the flock shrinks, it actually gets easier.
A few ideas... maybe as the flock shrinks the speed increases? Or it just increases over time?
Or maybe some other penalty as the flock shrinks? As it currently stands, it's easier to just thin out your flock right away rather than protect them.
One thing I've been seeing in a lot of 109's games is a sense of futility and impending failure, which is pretty interesting! Your game has that feel, but maybe needs a little more urgency or impact especially as it goes on.