many people consider this a great degree of freedom and an achievement. i call it downtime.
what do you think. did the terrain kill the old school level design?
Well I think it's not as simple as that and the terrain feature doesn't really have anything to do with this. Stalker just is a totally different game - you just don't follow pre set routes (as you said mostly indoor and if not you're in a tubular trench or something) but can walk "everywhere" and explore as you want. This can be connected to the downsides you mentioned but it also has its upsides - it's probably up to your personal taste what you prefer...
So I wouldn't call the terrain a design killer but just a huge possibility for different games. I mean imagine thinks like Operation Flashpoint or the Battlefield series without outdoor terrains - it just wouldn't work at all in an indoor environment. Terrain is just a feature and it won't work with every game type. With that said using big open terrains wouldn't be of much use in a game like Jedi Outcast (I guess this is what you consider as JKII) just as it's for games like F.E.A.R. or Max Payne. I think there are a couple of games which succesfully combined an open terrain with a highly linear gameplay and that would be games like Half-Life 2 or Quake 4. In those games you're not always in an indoor environment but also outside on a terrain. It still keeps that linear gameplay though by for example making you just drive down that aqueduct or however you may call it in Half-Life 2 and Quake 4 also only has extremely linear outdoor areas where you immediately know which way to go in order to advance...
So it's up to you as designer and your game. Terrains aren't of much use for linear, "story-based" shooters but for Multiplayer or games with a focus on exploration you'll really want to use something like that if it fits your design...
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