The thing about Colonies is that they're very expensive. Sure, you usually win if you get 6 colonies, but that costs $66. Meanwhile, someone who gets all 8 provinces will only spend $64. All of the Duchies and Dukes cost $80, but it's a lot easier to come up with $5 turns, plus you can gain Duchies and Dukes from other cards like Altar, Count, Upgrade, etc. Similar arguments apply to other alt-VP cards. Plus, it's a lot easier to come up with an engine that buys multiple Alt-VP cards every turn than to consistently get $11 or more.
In some Colony games, Colonies will indeed be the dominant strategy. But I've played plenty of Colony games where fewer than 3 Colonies were ever bought, because another strategy was faster. Making Colonies worth fewer VP would decrease the number of games in which they are worth buying--and in games where they are worth buying, they're still available to everyone.