Snoopy and Dale have been working on a PatchMod to resolve the bugs in the game, rebalance certain parts, and make the game the 5/5 it deserves. 
This is separate to the unofficial patch which addresses bug-fixes only.
Current version 1.07
Please download the latest version from here.
Installation:
1. Download the patch.
2. Open the actual game folder (default is C:\Program Files\Sid Meiers Colonization\) not the "My Games" folder.
3. Create a folder called "Mods".
4. Open the Mods folder (C:\Program Files\Sid Meiers Colonization\Mods).
5. Unzip the PatchMods to there (it should create a new folder in there called PatchMod: \Mods\PatchMod\).
6. Open the new PatchMod folder and you will see an Assets, PublicMaps and CvGameCoreDLL folder, and the ini file.
7. Start Civ4 Col and load the mod by selecting ADVANCED --> LOAD A MOD and selecting PatchMod.
8. C4C will restart, and you'll know you're in the patch as top-right will indicate the mod's name.
List of changes:
Code:
PatchMod 1.07:
Fixes and Changes:
REF:
* Added iKingUnitThresholdPercent xml tag to Civ4HandicapInfos.xml and implemented. This allows the REF increases to be modified by an XML edit. This will currently be left at 100% (normal), until further testing can be done to determine appropriate levels. Increases base incremental percent (10%) by fraction of (value/100).
* Added iKingGoldThresholdPercent xml tag to Civ4HandicapInfos.xml and implemented. This allows the REF to change due to paying King money demands to be modified per difficulty (default == 50). This effects the REF threshold, rising it in relation to the amount of gold given to the King. This slows REF growth by kissing his pinky.
* King no longer increases taxes after WoI.
* King no longer increases REF after WoI.
* King no longer requests gold after WoI.
* Tax rises less often in Marathon and Epic games.
* King's navy cannot enter native settlements.
* Only coastal cities with specified good mentioned in party text.
* Can no longer bring up domestic advisor during diplomacy.
AI:
* AI will now use King's Transports after turn 90 for treasures if it doesn't have a galleon
* AI will load and take treasure to Europe from uncolonised continents (before they just sat there forever).
* AI now arms units in Europe and transports them to become standing defenders of the colonies.
* AI now correctly pursues massive armament during lead-up to revolution (previously only did this on declaration of independance meaning it only got one turn to buy an army).
* AI is now capable of winning Indian wars and the War of Independance
NEW * AI has more cash for everything.
NEW * AI now capable of having more than 2 transport ships (now max 5).
EDUCATION:
* Reduced education threshold increase from 20% to 10%.
* Multiple colonists can graduate each turn.
MAPS:
* AI start locs no longer in order from top to bottom of map (randomised).
* Humans no longer start in the same start loc.
* Europe Sea Zone fix to one third of the way in from the map edge and 4 tiles from coast
* Regenerating map now resets REF (previously, every regeneration increased REF by initial size. EG: 8/4/4/4 to 16/8/8/8).
* Europe sea zone now removed from map when plot erased (noticeable in Map Regeneration).
* Start locations on random maps spread out more (increased iRange index from 10 to 40 in CvPlayer::startingPlotRange()).
* Can now sail to the east or west coast (if known) from Europe.
* AI will settle correctly in user-made custom scenarios.
UNITS:
* Colonists can now join cities after moving (like founding cities). Does not include outside jobs such as scout, military, pioneer, missionary.
* Can now set profession after moving (like clear profession).
* Converted native can no longer be educated at Indian settlements (can be trained at school as normal).
* Converted natives can no longer become missionaries.
* Units cannot be made a soldier/dragoon and attack the same turn (eliminates an exploit).
* Terrain double movement from promotions now works fully (eg: Swamp Fox II wasn't applying to marsh even though it was set to).
* Units unstack when entering native training (eliminates screwy behaviour).
* Units unstack when going to/from Europe (eliminates screwy behaviour).
* Easier to get Great Generals in Marathon and Epic games.
* Units on the way to, or in Europe get intercepted by the King when you declare independance.
* Defensive bonus for armed natives fixed to match unarmed natives (mounted/unmounted reversed).
* Docks hurry costs have a set maximum (currently 2000, will change).
NEW * That bloody unit cycling bug has been found, squashed and celebrated!
NEW * Automation (and AI) will no longer remove features from a plot when that plot is being worked and it has an improvement (eg: lodge on forest will NOT be removed under automation).
TRADE:
* European horses tripled in price.
* Blockaded goods no longer counted against tax rise threshold.
* King's blockades now clear after WoI.
* Warehouse expansion sales now count towards total traded amounts (not previously counted).
* Natives only change desired good when supplied with that good (previously was any good would reset desired good).
* Buttons on trade route screen corrected.
NEW * Prices in Europe are checked after each trade instead of only once per turn.
NEW * Production now calculated before resource yield calculation, fixes depletion bug.
INTERFACE:
* Warnings: Out of raw good for processing warning.
* Warnings: Almost out of space warning.
PEDIA:
* GG concept entry no longer talks about free upgrades and retaining full experience when doing so.
* FF's and Traits boosting native relations now correctly mentions auto-peace with natives.
* Renamed to Colonizopedia as it was in Col1.
* setBasicUnitHelp bug shows correct transport unit when changed from default.
MISC:
* Cargo now takes the number of berths in ships as defined in Civ4UnitInfos.xml via tag iBerthSize. (EG: Treasure now fills 6 berths of a ship)
* Can't declare war against another European Civ for the first 20 turns.
* Missionaries now produce converts for a PLAYER not a NATION (eliminates converts confused which player to go to when two players same nation).
* Exploration points now correctly scale for gamespeed.
* Pilgrim king gives you a free ship if you lose your final ship (regardless of gold remaining).
* Establishing missions now have an increasing failure chance based on success missions and difficulty.
NEW * Failed missions will have a negative impact on the Natives.
* Immigration threshold increase reduced to 20% (was 25%).
NEW * End of game now extended after first DoI (like Col1) based on GameSpeed: 75/100/150/300 turns. So now 300 turns to DoI, +100 turns to win from that point (on Normal speed).
NEW * Start location (re-spawn location) is now randomised each time you lose your last ship.
NEW * Text when Indians "give" you their city changed for clarity.
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