I guess you're expanding too fast, ProPain. I already try and keep my science ratio on or around 50%. My rule of thumb is not to build cities when the science rate is below 50%, unless it's important and you're afraid someone else will claim that piece of land. I sometimes even have a settler ready and only settle on the moment I see the AI approaching with his settler.
Oh, and of course learn the use of Courthouses! (And therefore Code of Laws.) Having Currency also makes quite a difference, because of that extra trade route in every city.
Personally I also do have the tendency to emphase to much on production and too little on commerce. I.e.: I should build more cottages. Perhaps you should too?
I do agree Warlords isn't worth much. It's highest value is that you can play with other people who also got Warlords.
I even select "no vassal states" nowadays, because I really don't see that value in that. It's actually kind of annoying that so many useless small civs stay alive until the end of the game. They only make the game runs slower. (Makes a difference on huge maps!)