I think the clones are fine as they are.
CDITDZ is a very hard game in itself; it was designed that way.
I believe that clones will not change, as for now, they are in their suitable spot.
By the way, here's some reasons to why your fixing ideas might be rejected:
1. If you did this, you would essentially have infinite clones, which could make the game too easy.
also you'd be able to get 5 upgrades per level, which is no good
2. I visualised this a while ago, but I rejected it in the form of being too harsh. Of course, back then, I wasn't thinking of the updating. Personally, I don't think that the updating would work, simply because of having too many clones. If it reset the clones, this still wouldn't be a suitable option, as instead of updating, you could simply get a new one and save the luxuries for later.
You'd also have more backup plans.
This idea is more of a 'hard-mode' idea if you don't include the updating (which would be very complicated, too complicated for the human's tiny minds)