A long-time player, this is my first post here. I hope someone takes these to heart!
1. Cities should not take up a whole tile, except perhaps for VERY large cities, only possible late in the game. This is also the case with the "cottage/hamlet/village/town" tile improvement. All of these should be able to coexist with other (agricultural or other) improvements on a tile, at least up to the modern era. Before a mass transit system (MTS) is built, a city should not take up more than ~16% of a tile, at roughly 1% per city size. A MTS would enable the city to exceed size 16, but increases city area by 2% per pop size above that when built. The discovery of combustion/automobile boosts this to 3% and, finally, with a new city improvement, such as a FREEWAY boosts this to 4%. This way, only a HUGE city (size 25 or bigger) with the previously mentioned improvements would actually encompass an entire map tile. Of course, until a city reaches this size, it could not act as a canal for ships. Instead, another city improvement (CANAL) would enable ships to pass between two bodies of water within the city's 3x3 zone. Cottages should be able to be built on tiles with (any) other improvements, providing a trade bonus from the tile. Late in the game, a town should also potentially grow into a periphery city/suburb. With cities and towns/suburbs, the area taken up would reduce the productivity of the other improvement (at least food and hammers), though commerce would replace them.
2. Get rid of fixed food resources (like banana, wheat, corn, sheep etc.) to tiles. This is plain silly. While crop wild relatives should be fixed in place, once domesticated, these all should be able to be planted/grown on any food production improvement (and wild resources disappear once improved). If you can trade for them, then you can grow them anywhere. Wild relatives of livestock should roam around like the beasts do, and warriors or other units can hunt them, reducing their "strength" while providing food bonuses (similar to clearing forests do for production). Repeated hunting by powerful units (riflemen or higher) run the chance of eliminating these "food units" as does improving tiles. Once too few unimproved contiguous tiles exist to support the wildlife, they go extinct. Like crops, these could be domesticated and raised on tiles and/or traded. Other resources (like corn or small grains) should be able to be used to boost the productivity of livestock-rearing tiles.
2b. Several new crops and livestock should be introduced including small grains (barley, oats, and rye), millet and sorghum, citrus, stone fruit, tobacco, flax, hemp, soybean, sunflower, peanut, palm (oil), and jute. Also, coffee, cacao, tea, olives, pecans, walnuts, chestnuts, filberts, cashews, almonds, pistachio, dates, and, finally, RUBBER. Each would provide bonuses that would only be maximized if grown on the right kind of tile (see below), though some (like rubber) can be wild-harvested to some extent. Cow should be differentiated into dairy (requiring grassland, pasture, and surplus oats/barley) and meat (requiring any terrain with surplus grain), each providing different bonuses. Additional bonuses (happiness and health) would come from the number of different crops cultivated by a civ.
3.Terrains should possess additional characteristics:
a)altitude (lowlands, uplands, and alpine) to enable plateaus, alpine valleys, etc. This would modify the...
b) temperature regime, consisting of two seasons, including hot, mild, cool, and cold
c) precipitation regime, also consisting of two seasons, including wet, humid, and dry.
Cumulatively, these would determine (1) natural vegetation/biome, (2) what crops can be grown (without irrigation), and (3) whether/how fast forests/natural veg. regrows when unworked by a city.
Oh, and JUNGLES should not be so worthless!
4. The "farm" improvement should not be able to be built until Emancipation civic is adopted. Prior to emancipation, crops and livestock would be raised on villa/manor/estate/plantation. Of course, cities still working these some # of turns after emancipation is adopted would revolt until replaced with farms. State property civic would (1) prevent city revolt following emancipation, (2) convert plantations/villas into farms without workers doing it, and (3) provide bonuses in between the farm and the estate (more $ but less food than a farm).
5. I've heard that Civ 5 will make resources finite. While this is a great addition, I sincerely hope that all are not equal. Mesabi and Michigan iron deposits are VASTLY larger than Birmingham or Cedar City ones. PLEASE say they will be unique, each with variable quantities of mineral resources, that can be set or randomized.
6. Some new mineral resources need introduction:
Tin (crucial to make bronze, very important prior to bauxite processing/aluminum)
Lead (crucial for batteries, bullets, and radiation shielding)
Zinc (crucial to make brass)
Mineral fertilizers (phosphate, potash, sulfur/pyrite) boost agricultural productivity
Ferroalloys (manganese, nickel, chromite, cobalt, tungsten, vanadium, and molybdenum) could come from general mines once metallurgy (nickel, cobalt) and steel (all others) is discovered. Which particular ferroalloys a civ posesses effects armor strength
Coal: Bituminous, lignite, and anthracite, each with unique bonuses to productivity
Miscellaneous:
Oil requires refinery to produce fuels.
Uranium requires centrifuge to produce fuels
There's my two cents. Would love some feedback!
-J
for about 5-10 turns as the city deals with the fact that a massive nuclear explosion just hit it. 
