I think the main problem with this game is that it is too good for you too have many colonies. And once you have like 6-10 colonies the game requies too much micro management so it stopps becoming fun and more fun to just start a new game.

I think the game needs some mechanics that will give you penalties to have too many colonies. I know that it's harder to defend many cities during an independence war, but still.

My suggestions:

It feels like special resources had a larger bonus in the original, than here. So it was only worth building a colony near 2 or more special resources. An extreme example, an iron on a grassland only produces 2 iron, less than an hill without iron :p
Perhaps they could be abit more powerful, relative normal land.

Some upkeep cost for having lots of economies. Like: First colony requies no upkeep, 2nd costs 1g each turn, having 3 colonies cost 3 g each turn, 4 cities costs 6 each turn, 5 cities cost 10g each turn... (totally)
It would be nice as an inflation reducing effect too.

Lots of land/colonies doesn't necessarily get you much since your supply of colonists is finite and the upgraded buildings represent a large increase over the base buildings. The colonies are pretty much self-sustaining in that each colonist is contributing with labor and there really isn't any bureaucratic overhead that requires funding. With limited resources available establishing an outpost and requiring someone to remain and defend it, not to mention the need to transport any goods elsewhere, needs to make sense.

the mechanic also is the liberty bell generation. Having lots of colonies will take a loooong time to build up rebel sentament

A larger colonial empire is more difficult to defend, it also takes more time to get ready for the revolution and time is finite.

And once you have like 6-10 colonies the game requies too much micro management so it stopps becoming fun and more fun to just start a new game.

Very strange. It's the most intresting in ECONOMY/strategy game that Colonization is. To organize it good.
I think you just do not know about Trade Routes and autometed transports :) Or still can't use them well.

And by the way - there already done penalty for many colonies...
Hard to management and hard to defend big colony. It's still from Col1. I think it's nice if you can have big colony with it's problems (if you can handle them) or small and effective.

In Col2 there second limiting factor - the size of REF and the way it's calculating. I hate it.