@ Virupaksha: Cities gaining whipping-anger over the course of the game is not unusual and you can work against this, by simply conquering as many happy-resources that they still stay happy. REP also gives you +3

in the biggest 5 cities and if anything fails, you simply 4-pop-whip a Market for 4 extra

. Also later, whips are 3 and 4pop, then the anger reduces automatically. What I suspect, is, that your cities are simply to big, it's not really difficult to keep a size 4-6 city happy, and for Dom- / Conquest, only the capital should or needs to grow large. I wrote a guide on city-management, don't know which issue of CIV Illustrated it was, but you'll know when you look at the names of them, I listed them in my signature and you can also find them in the Strategy-guide's subsection.
And the reason why non-riverside-Cottages outside of the capital are so terrible, is because every point of population also increases the maintenance. On Deity, a point doesn't cost 1GPT, but it's not far away from that sometimes, if a tile only gives 1GNP, it's basically giving almost nothing. Non-riverside Cottages in the capital are also only really worth it once they've grown to Villages or maybe Hamlets if including the bonus from Buro.
And Plains shouldn't be worked before the late-game-techs of Biology or State-Property. Lots of players made calculations on that, me too. Working Plains often costs

, more than the Plains-tile gives. 1

is easily 1.5-2

via the whip, Plains cost 1

so they cost 1.5-2

, as they give 1

, that's a netto-loss of 0.5-1

/ turn.