I loved your game, but yeah this is a problem you inevitably fall into. Why not give the player the option to save a dice when they don't need it for exemple, either using replacing a dice later with it, or just giving its color to a dice, or maybe even choose the color of a dice before you roll the three ? It woud give another layer of strategy since you have to perform well enough first to be able to play a round with just two die, and then give you a tool to escape those impossible rounds (the three blue die when you get two stacked rows of enemies is a feelbad game over).
Maybe even a special power up that lets you chose the color of the three die before rolling, that fills up with combo points, incentivizing the player to take more risks to create rounds where they wipe a lot of enemies at once, rather than just try to kill the most enemies every round. In general combos being accounted for seem like a good twist, even just a blue and green line intersecting with +1 damage might be fun.
It felt very good to create openings strategically in lines rather than do the most damage overall for exemple, because it probably means you'll do a lot more at the next round with red or blue die.
It's a very fun game already and it seems like there could be plently of ways for you to twist it into something more, so bravo really, very good stuff and I hope you keep working on it, it'd definitely buy it as a finished game !