Hey, thanks for taking the time to write such a long comment and give such detailed feedback. I've had people mentioning this problem to me before with similar suggestions of solutions. I'm really not keen on making the tiles enter from a different directions, for a few reasons:
1. The metaphor of match-3 games with tiles falling from the top is incredibly important to me. Not breaking this expectation goes a very long way to making the game easier to pick up and understand.
2. Since the very beginning, one of the main challenges of the game has been keeping your towers up, constantly reshuffling for an optimal ordering.
However, I do agree that there may be an issue here, I just don't think the solution is to change the direction of the falling. It's probably also a question of balance, where I haven't made the horizontal shooting towers strong enough / vertical shooting ones weak enough.
As for your second point, I don't think that allowing enemies to destroy every tower will be a particularly fun experience, and I agree with you that the feedback loop will make the game very hard.