If HAR planets had maybe, a wind current that always went clockwise/counter-clockwise, then I can imagine a whole lot of possibilities. Imagine, you see the last snake egg that you need! But, you realize it's unreachable because of the gust pushing you away from it. So, you have to either: 1. Build a drone that can work with the gust, or 2. Build a drone that can work against the gust. I think that while still tedious, it would add diversity, and I would no longer ignore HAR planets. Instead, they might be my first choice to play on!
As for the whole "Why wouldn't thrusters work underwater," I'd have to both agree and disagree with Ookami, it doesn't really make sense, but at the same time, how the heck do you explain this game's magnets? Obviously, the game should be realistic, but I don't think it should just be a physics simulator. The strange little quirks are what brought me to this game in the first place. I can totally see something silly like a propeller in this game, just because it doesn't really seem too out of place.
Before I go, I'd like to say a few things. Many people in this thread have suggested great ideas to balance the propellers, but the one that I really like the most is the AR gradient. It'd require the use of both propellers and thrusters, but at different levels and on different planets. Alright, last thing! As I said before, i feel like there's no real reason to play a level that's not fun. I'd still like a level to have a use, even if it's not fun; I'd still play it, and I would likely get so fed up with it that I just adapt. This 'reason' I think that everyone would like, even if they don't know it, is the return of green resource. You could get it from planets and from sumo arenas, but only once, after you complete the mission. The amount you get would scale to the difficulty, and it could be some tiny amount or a ton. If the drone part limit Is added, then green could be used to expand the limit, bit by bit. If it isn't, then it could be used to unlock upgrades in your techtree that can't be unlocked any other way.
Well, that's all I have to say.