Played to mid 17th century on satuday using accelerated start. No serious bugs nor any crashes encountered. Here's some observations :
Problems :
Treasure (or units with it) can't be given goto orders as they forget it next turn. (Actually this seem only apply if you give goto order right clicking destination with mouse.)
You can’t manually move land unit to last row of tiles next to western map edge, how ever units under explore order do not have this limit.
Wagon trains can not be loaded rendering inland cities useless for anything else other than building units. This is especially bad because best building spots and most of the hills are inland.
Units can’t be give explore orders unless they are one square away from unexplored square. This means if they stumble into ruin that gives map of surrounding territory their orders are cancelled.
Currently higher level ships can not be build due to their high resource requirements and limited store capacity (galleon requires 800 wood but you can only store 250). You need to allow cities to start building things with fewer resources than things require to complete. Maybe deduct only fraction of resources each turn (thing need 100 wood to complete and takes 4 turns to build. Make it consume only 25 wood per turn.)
There are quite few typos in encyclopedia. You should run some simple spell checker to fix the most obvious ones. Or I can do it when I have time if you want me to. (not too important as game is far from complete).
Balance issues :
You'll need to make colonies add some free upkeep, make colonies produce some limited amount of cash or reduce unit upkeep otherwise its almost impossible to upkeep armies (my 2 caravels and galleon can barely move enough goods to upkeep one army strong enough to take an Indian village). Also Indians can field way too large armies (fixing this may be enough for now. It should not take move than 4-6 units to take out normal native settlement.). These problems will only escalate when you add fluctuating prices of goods and the need to defend colonies (AI).
Crown tax increase will need to be toned down. It should somehow be tied to expansion (and profits) of colonies. Same goes eventually to royal expeditionary force. (Crown needs bigger ref to ‘protect’ the colonies so it needs to increase taxes.).
Improvements & suggestions:
Remove inland cities from naval unit goto list.
Remove sea related buildings from inland city building list.
Allow upgrading of dry docks, chapels and similar buildings instead of having the higher level buildings as separate buildings (and higher level production buildings should have the effects of lower level as well if it's not already that way). Also allow only single building of type per city.
Swap building level of stables and windmill so inland cities can increase food production at level 1 the same way as coast ones.
When renaming colony in colony screen put the old name in renaming box in case player just want to correct spelling error (the ‘b’ for building colony sometimes gets added to end of new colony name).
Add option to load game from start screen.
Encyclopedia needs better browsing options eventually. (See the ones in similar games.).
Units with explore orders should not enter Indian settlements (at least not until contact with Indians will be possible).
Add sell/unload all button to Europe screen.
Have you experimented with allowing full army battles (allowing all units involved to participate in battle at once)? Maybe it would be good idea to add hostile fortified colonies, armies and fleets for testing combat against them?
Question :
What does factory do (or what will it do)?
Does difficulty currently have any effect (without the AI)?
Great work overall! I'm surprised how stable it's been (I've tested quite few games in progress and most tend to crash one place or another sooner or later (Well Landfall did too when it was realtime)). After remaining missing features are implemented you'll get to the hard part of implementing the AI

.