First off, absolutely love this game. I have spent tons of time playing it!
While playing, I thought up some general things that would be nice, thought I would throw them out here. Some of these may be out there already, but I could not find a roadmap or anything like that.
Cures (Actual Cures) - Ever get it in your head that you want to be a benevolent company and make the world a better place? Then you set your sights on wiping something out, you watch the progress as it gets closer and closer to 0, only to find out that you cannot ever really get rid of it. I wish you could wipe out something completely if you wanted to.
Another speed - sometimes you just need to speed the game up, there have been times when I know I am going to win a scenario, and I just need to wait for 500 successful cures or something like that. I end up sitting there for a while just waiting, a third speed setting that goes by multiple days at a tick would be nice.
Move Inputs - It would be nice to be able to pay some crazy price to move an input. Sometimes you just need that input moved 1 or 2 spots to be really useful.
Dump drugs - having to use an analyzer at one side of a centrifuge is not intuitive. It also adds cost to something that should be really be free, or at least cheaper. If the player really wants to they can Ctrl+click to remove the drugs from the line for free.
Speed Lines - Ever have to move an input from halfway across a floor to combine it? While a giant line of ingredients might look cool, sometimes waiting an entire month to get that first one to the machine is not great. It would be nice to have lines that move things much faster but cost more.
Discovery Time - I think that putting how long it will take to discover an ingredient would be nice. We have this on the research pane, we know it takes exactly X months of research to unlock something, but the discovery pane is like an enigma.
Extra workers - Sometimes throwing more bodies at a problem is the solution! Being able to add extra scientist or explorers to a task should decrease the time it takes to unlock it. Maybe up to a limit, like twice as fast or something.
Ship to another factory - This one may be crazy, it was an out there idea I had, but I was trying to put together a drug with 4 of the best cures I could get and I ran out of room in the factory I was in. I was looking at the screen and I thought it sure would be nice if I could just send this out that port, but instead of trying to sell it, have it sent to another factory of mine to work on it some more. Then I got to thinking that this would also be useful when you have a little space to do a small part of a bigger drug, you could do one part of it, export it, then import it somewhere else.
Change research points quick view - The idea is great, but limiting it to 9+ is annoying when you have things that cost 16 points. I find that I end up ignoring it because I get tired of clicking over to the research pane to see how many I have, then when I do check I have like 40 points. I think that the quick view blob should at least show up to the most expensive cost to unlock something. Same for ingredients.
I am almost done with the last of the scenarios which is when I plan on looking at some of the mods. Maybe some of this stuff is covered in a Mod already or something, but wanted to maybe throw out my ideas that I thought would help the game be even more awesome than it already is.