I lack the skills but would love to help out some way. Please let me know if you have any simple but annoying or tedious tasks that I could chew through. Here are some of my thoughts -
Phase 1: The tech tree really needs some help. I liked Civ IV Tech tree and I would use that as a model.
a.) Rename "Penicillin" to "Modern Medicine" or "Western Medicine." The technology for discovering penicillin existed prior to its discovery. What made penicillin so important in the 20th century is that it was mass produced and was the advent of the pharmaceutical industry.
You could have "Modern Medicine" as a researchable tech and "Penicillin" as a random event. For example, after "Modern Medicine" is teched, "A scientist working in a forest near Corinth has discovered Penicillin (+1 Population)."
http://en.wikipedia.org/wiki/History_of_penicillin
b.) bring back "Artillery" and expand "Dynamite." Artillery is a tricky one, because cannons are artillery. You could have artillery as an earlier tech and then as newer techs are discovered (gunpowder, dynamite, etc) existing artillery units can be upgraded.
Dynamite makes nitroglycerin stable. In addition to warfare, dyanamite's used for building roads, developing mines/quarries (blowing up mountains). Dynamite should add some bonuses to production (mines/quarries), reduce build time for roads/railroads, and maybe even boost population since it is a safer way to use explosives.
http://en.wikipedia.org/wiki/Dynamite http://en.wikipedia.org/wiki/Artillery
Phase 2: Redesigned improvements
a) the windmill is a tile enhancement, not a building!
b) bring back town development
c) make solar panel a tile improvement in desert
Phase 3: Miscellaneous
a) Resources - rework and expand resources. There are too few crop (rice, corn, potato, etc), livestock (goats are huge IRL!), and ocean (crab, clam, etc) resources. Those additional resources don't really need special bonuses, but add some diversity to the game.
b) Expand resource gameplay - Crops and livestock developed with mankind and their cultivation was traded amongst civilizations. E.g. Potatoes are a New World crop. If food resources are isolated around the map then civs could trade for a new crop's seed to expand their food resources (after completing a trade for potato seed, a potato resource pops up somewhere in the civilization. Random events could lead to a new food resource popping up ("While exploring near Grand Rapids, your scout brought back corn seeds for the city of London.") for a civ leading to a more diverse food supply. Diverse food resources lead to population or happy bonus.