Well, it is fixable without changing the drop rate by very much at all. If something has a 1% drop chance, you could make it so that every 100 kills, it is guaranteed to drop -- if it drops before that, this counter is reset. That puts an upper limit on the drop chance. If you didn't want to deal with such counters, then you could have it automatically drop every 200 kills, which does increase the drop chance a bit, but not too bad. Worst case, adjust the drop rate accordingly. If the drop chance becomes 0.5%, but every 200 kills it will always drop (no counters), then that's on average the same 1 in 100 rate as before -- yet it is far less random. Best part is that enemy kills are already kept track of, so the amount of coding needed is relatively small.
As for mechanics, I think the biggest thing I want is the phasing out of wires in favor of Starbound-like wireless connections -- "wires" are still there in a sense, but they aren't an actual item. You click on one point and run a wire to another point you click on. In the code only the connections matter, so wires can criss-cross without issue. It wouldn't be hard to keep the current wires in while moving two a new system, I think.