The point isn't moot at all. That upgrade is optional after being spoon-fed to the mechanics which continue to vary throughout the game. until then, it is locked. You are given curve balls with an evolving experience in almost every respect. Right down to the texture and model work.
No son, this is over-powered. With AI that makes Arkam Citys look like Albert Einstein.
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This is cheap. And a good example of the problems of linear gameplay hitting non-linear. As well as just plain bad design.
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In Arkham City even when using instant take-downs you are being forced to move around. The game actively encourages you to use the arsenal at your disposal with an enviroment that changes from area to area. The gadgets themselfs are gimped. You can only disable two guns. Two mines, gargoyles can only be used once. Gas can only be used once in an area. This limitation is a good thing . it encourages you to play around and experiment.
You seem to be discounting is that the actual level design also alters...
Rocksteady deliberately remove gargoyles. Area's have specific cases in which you only get a jump advantage via stealth but then are forced to resort to combat. Cases in which you are not allowed to set off any alarms. There are also specific Riddler related NPC's which the game encourages to leave till last. Area's mined. NPC's walking around with scramblers that cease the use of detective mode. There is also alot of specific NPC's you cannot stealth against at all such as the league of shadows, which also prevents gliding kicking and throwing objects. Hell, when fighting freeze the game outright says "no you, are not doing that again" forcing you to move around the map altering methodes. Even though he is incredibly easy.
Arkham City has done almost everything right to avoid the feeling of redundantly doing the same thing over and over. To be cheap in this game, you need to go out of your way. The main problem in the outside area is that you dive bomb over and over. To be cheap in Skyrim, you really don't need to try at all. It's part of the game design.