First some general bugs:
1)Dragoons are not listed anywhere. Not in the col paedia or in any stat screens.
Now some things I noticed in a Spain game on the highest difficulty level:
I declared Independence at turn 180 with 11500 pop and 26000 soldiers. Those numbers are a bit wacky, I guess 100 pop is 1 colonist, but the soldier number does not make a lot of sense. In fact the size of the Ref force is 105000, about ten times my population, which does seem a bit excessive

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1) Prices in Europe seem to be completely fixed. I purchased more than 3000 horses and never produced a single tool until the declaration of independence on turn 180 and prices stayed at 3/4.
I also specialized in a tobacco/cigar economy, producing from two factories with 3 masters each and the price is about the same for cigars/rum/cloth/coats
at 11/11/12/12 each.
As a result ore miners/blacksmiths/master ranchers are all pretty much worthlerss, because it is not worthwile to produce the stuff yourself and there is no point in diversifying your goods except for space reasons.
2) Probably more of a balance issue, but founding father balance is completely crazy. Some are almost worthless and Peter Minuit the first trade FF is better than all exploration FFs combined.
3) Speaking of founding fathers, it is annoying that you don't get the chance to get one again when you pass him up once. Often I want a different one first than the one the program offers me, but after saying no once I never get the chance to get him again even after hitting his threshold again.
4) The AI of the other colonial powers is pretty worthless even on the highest difficulty level. I had no problem at all killing the English right from the start. France got massacred by the Aztecs and Holland managed to declare Indepence and is slowly losing the war. The only trouble I got were two privateers, which managed to kill my starting caravel.
I suspect they perform so poorly, because they seem to blow all their cash on colony buildings. You often find a lumbermill in a settlement that you capture in the first ten turns. Rushbuying stuff is a good thing in civ4, but it kills you in col.
5) No sugar resource anywhere on a large map.