I did a search on the forums and couldn't find anything on this suggestion so forgive me if this has already been suggested.
First off, I love the game and have had it at least for over a year now.
The most frustrating part of it is how the research is dealt with. It's just a giant group of boxes and you get to pick one. This really needs to be a tech tree with clear definable paths and prerequisites.
Just a suggestion on what some groupings/paths could be:
Weapons, Armor, Mobility/Trains/Cars, Logistics/Conveyors, Smelting/Furnaces, Robotics, Construction/Factories/Oil/Upgrades, Energy
I could go into more detail, but I think anyone who's played the game knows what I'm getting at.
Problems this could solve:
Getting Prompted in the middle of an attack on alien spawns or getting attacked by rabid alien dogs. How? Because when you pick a research, it will queue up everything in order to get there. Also, getting prompted is super annoying, just put some blinking, bold, red text in the upper right corner of the screen saying "No Research Selected" where the research bar usually goes.
You could take this chance to revamp all of the research options to single each one out individually, because lets face it, the research is the backbone of the game and the main objective (besides not dying).
Energy
Windmills and more efficient solar panels would be great additions. Having miles and miles of solar panels seems excessive and monotonous.
Speaking of trees, are we ever going to be able to plant trees to reduce pollution? It would be cool to see pollution kill trees once they've soaked up so much. Like tick down their hp as they soak it up.
Happy gaming!
Tech Tree
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Re: Tech Tree
They've redone the tech tree / research screen, it'll be in 0.13 afaik.
https://www.factorio.com/blog/post/fff-128
https://www.factorio.com/blog/post/fff-128
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Re: Tech Tree
I agree this being prompted is annoying. But it can be turned off in options. 
See also this mod: viewtopic.php?f=92&t=17219 Research queue 1.2.4
The solar panel thread: Look into the balancing board, they discuss now since months about such things.
The trees: The devs planed that. It's already the case, that the tress get dark and ill.

See also this mod: viewtopic.php?f=92&t=17219 Research queue 1.2.4
The solar panel thread: Look into the balancing board, they discuss now since months about such things.

The trees: The devs planed that. It's already the case, that the tress get dark and ill.
Cool suggestion: Eatable MOUSE-pointers.
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I still like small signatures...