-start the timer when the trapdoors are open NOT when the level begins
No, it's better to let it like normally. For all lemmings games, timer started when the level began.
-have the choice wheather to have amount to save shown as a number or a percentage
No! I prefer the number to save instead of a percentage. It's easier to see how many we have to save. If you put percentage: Imagine that you have to save 75% and then almost all lemmings are in the exit and you don't know how many died during the level. Then there's only 1 lemming left and you saved 72%. So, is that lemming counts for 1%, 2%, 3%? It depends on the number of lemmings in the level. And... A0;X_X
No, please, keep the number!
-no replay glitches
-have the ability to play .dat and .lvl (lemedit) files
No, wait! LemEdit levels aren't compatible for Cheapo. The reason why is that levels of LemEdit uses specific graphic set and sets all terrain pieces in coordonates on the level. I don't know, really don't know, if it would be compatible on Cheapo... but if it is, it could be really hard to do. What do you think about that Peter?
Oh! And here's another suggestion:
Imagine you have to save all lemmings and then 1 lemming died. That way, you know that you failed the level. Why not putting a small window with this text inside when the game look that there's not enough lemming to complete the level:
"You failed the level! There's not enough lemmings to complete the level!"
Then, right under, put 2 buttons:
"Nuke them all and restart" + "Continue anyway"
Also, in the options of the game, turn on/off this window! What do you think about this?