Okay, so I was away from the forum for a while and didn't know about the "no bonus for settling on a resource" change until just recently. Is that a change to the SVN? I'm playing version 1.12 and didn't notice the change, so I'm assuming it's new for the SVN.
I read through a lot of the back-and-forth, and saw good arguments on both sides. On the one hand, settling on resources provides a massive early bonus to civs that can be pretty easily exploited by folks like youtien. On the other hand, though, the new rule that eliminates the old resource bonuses on city tiles means players must try to settle on non-resource tiles. This not only sharply limits where cities can be placed for best effect, but also incentivizes ahistorical settlement and expansion (since cities historically were founded near high-productivity areas which we represent by resources).
I would suggest a compromise. The main problem with the resource bonus is that it gave a lot more

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from very early on, without having to wait the turns needed to build a worker and have him improve the tile. So why not create a delay, between when the city is founded and when it receives the resource bonus?
City tiles are automatically worked in the BFC screen. Treat that imaginary 1-population as though it were a worker; then you'd just have to wait the requisite number of turns before the resource comes online. Later in the game, the number of turns would be affected by normal changes (from wonders, techs, buildings, etc.) that affect worker rates. If "city-tile pop = 1 worker" is too much, treat it like half a worker, and double the number of turns required. Another possibility would be if the city didn't use its normal 1-population to work a tile outside the city, but instead kept it as a civilian specialist (default +1

). You could treat that specialist as a city-tile worker and decrease the number of turns required as a result.
Basically, if the main problem is with the insta-bonus, nerf the "insta" but keep the bonus. Thoughts?
EDIT: Just after I posted this, I had another thought. What if, instead, we treated the tile improvement as though it were a building? Add a slot or slots for farm/mine/town/etc., with requisite number of

and the necessary tech prerequisites to make it happen? This would, as above, nerf the insta-bonus while allowing for greater flexibility in terms of where cities can be founded. Recall that cities in DoC are not so much cities as they are stand-ins for regions -- it makes sense that all BFC resources could be exploited, even if they're on a city tile. The only trouble is making sure the bonus actually takes some effort.