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If "Piratez EXPECTS you to use it's full mechanics and features"... which I personally don't think it is... then it almost means there is "only one solution" (or only a very limited number of solutions) to the game. If you couldn't win the game with just 6-7 bases, or without air superiority, or without plasma weapons, or without using a certain soldier type, or without xxx (feel free to replace with any mechanic or feature you like here)... that wouldn't be the "greatness of its design', but its biggest flaw.
I haven't played Piratez for a long time, but I hope it didn't get to that point. That would be very sad. Judging just by what I hear from other players, there is a high replayability to the game. Also many say the game is easier than many other mods (and comparing my recent twots/area51 playthroughs with the older piratez playthrough, I would definitely agree).
I think I get what you're saying, I just think you're over-exaggerating quite a bit. Yes, the game expects you to think... but it doesn't force you to blindly follow "the most optimal path" (that would be the opposite of wanting you to think, no?)