To start with If playing a game for winning (at the highest! difficulty levels) is boring, its bad game design. (take civ4 as an example were its just the opposite)
If (at those levels) you actively have to play way subpar counter to knowledge (which is easily and fastly aplied without huge micromanagement) to have a fun game something is! wrong.
Now if you do so and get whacked real bad (on the lowest difficulty levels) in addition to that it gets frustrating (as said: especially for new players).
So you can't / shouldn't play to the game rules but the oposite is also all! bad? Sorry, that just doesn't work out for a company publishing commercial games.
The evil players destroy their own game experience / their fun because they don't play our perfectly good game as we intended! them to do. Yea...
I guess in that case the devs should take a big dose of your sig.

Its about having fun. Not about the player having to find a way hardly to have any chance for fun. Or to simulate history as accurately as possible (Our friends from Portugal (edit:+ Brazil of course

sorry for not mentioning you as well right away.)) might object to that claim anyways.

)
But that said we sure can agree its still big fun nontheless for some / a majority of us. And the core of the game / concept is a solid one. (And im sure we can agree that some people like and expect polished games on release. And rightly so.)
And what goes a long way in redeeming the whole thing for me is that they have given the community (they did help to establish and foster by designing decent games and the tools to modify them) the tools to fix it fast. (Thats why i do give them credit for allowing the community to fix it. Because they have made that easy. And always supported those modders with excellent tools+encouraging rules. Unlike say EA...

... Spore... Yea creativity... But don't dare to get a peek at our SDK... So much for moddability. And im not even a modder.)
Now i agree that col is not a warmonger-game.
Thats precisely why i dislike the REF/WoI part (and did in Col 1) and at least in a state like the game is now have no qualms to make that part of the game as small as possible (precisely because i don't want to be forced into an hour-long slug-fest). So it helps me have more fun personally (even though i won't use it in my very first game to that extent. But after that, you can bet i do.).
Now that sure dosn't work for anyone. Overall far to much thought has been put into the whole REF + FF deal imo neglecting other things.
But! the game is also at least partly geared towards multiplayer so thats not completely out of the picture. And can't be. Competative games need to offer an acceptable balance were even by using the mechanics to the hilt it still doesn't break the game / fun for them and their contestants.
But: The reason why you don't arm and defend your settlements at all is precisely down to the inactive AI and all-huggy natives. (and again: you don't need to do anything by yourselves. Just pay the natives to do it. No waste of precious workforce and no need to defend your settlements still. The result is just the same...)
Try that in multiplayer and try to make your point so forcefully again.
So while i share your overall point there is a better way to it then just black or white, isn't it? (Col 1 has accomplished that with you not beeing forced into constant warfare at least until the WoI without rewarding you or the AI for downright neglecting it.)