[quote]tl;dr
Look at the picture. Use that layout as a starting point for all TPSs, especially for use of cover.[/quote]
I'm here to tell you in no uncertain terms that SC:Conviction has the single best TPS controls of any game. Now, obviously some controls in particular don't make sense for some games. You wouldn't need mark and execute in GoW or ME3 (...or...well, that's another topic), for example. I want to specifically focus on the cover mechanic, mantling, aiming, and reloading.
Both GoW and ME3 (easy examples, I'll keep referencing them) have sticky cover and it's awful to get in and out of cover and to move around in cover. Ao2:40th had an amazing seamless cover system, but sometimes you wouldn't be as in cover as you thought, causing you to get shot as well as making mantling difficult at times, and moving from one cover to the next was not very intuitive.
SC:C is almost as easy to get into cover as Ao2, but much easier to stay in cover when needed and just as easy to get out of cover. GoW and ME3 each would perform at much better paces if they had adopted the hold-left-trigger cover system. Staying in cover in SC:C also provides a slight zoom and better accurracy, but zooming with a click of the RTS feels very normal, especially for us who play Halo games. Mantling and moving cover in SC:C works very similar to both GoW and ME3, except it's based on where you're looking, not which direction you're leaning.
As for reloading, the LTS as reload instead of crouch takes a little getting used to but eventually feels entirely natural since your thumb is almost always on the LTS. LB crouch again takes some getting used to, but quickly very natural, and better than the standard X button.
Obviously this wouldn't work for FPSs, but for TPSs, it's perfect. It puzzles and saddens me a little how underplayed this amazing control scheme is, considering how well it play. I think that it's implementation into future TPSs would be a world of good for the genre.
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tl;dr ?