Randomly losing Research Points

Whenever a bug crops up post-release, you should be able to find an option named Release a Patch with a price following it in parenthesis. This option shows up whenever you right click on any of your characters. It will patch the game and make your fans happy!

Kalec's answer has some good general points but misses the actual question a bit, so here goes:

First, all features improve the game if they're included. Some are mutually exclusive, though - you can't have stereo and surround sound, for example. Obviously in a case like that surround sound would be a better boost to game quality than stereo.

BUT: Each feature costs development time to implement, and you only have a limited amount of it. If the amount of features you're pushing into a given field requires more dev time than you've allocated, the overall quality of that field decreases -- you'll see a percentile value behind the field name. When that happens, you'll have to pick and choose which features are really important, or allocate more time to that field.

Bigger games have more dev time, so can fit more features simultaneously.