I find the mechanics of Republic Commando interesting. On the face of it, it's a basic FPS which uses the Unreal 2 engine. You can carry 5 weapons plus melee attack and you fight waves of droids and flying bugs. Underneath that, however, it is something a bit different.
At the heart of what makes Commando different is the squad combat mechanic. Instead of the usual lone commando setup, you are one of four and you can give your AI buddies orders to help out. So far, so unremarkable (although at the time perhaps not - I can't recall offhand when squad control started becoming a regular thing). The really nice part is the way the squad control mechanics are worked into the game.
Firstly, it is not a gimmick - rather it is a tool that is incredibly useful to progress. In a game such as Mass Effect 2 you can quite happily ignore your squad and they will do their own thing while you blast your way through the encounters, however attempting to do this in Commando this will likely result in a quick and messy death. On several occasions during my playthrough I blundered into a firefight and had my team slaughtered however on restarting the section, playing thoughtfully and actually using the options available to me the exact same encounter became a breeze. This isn't because your mates are victims of stupid and in dire need of micromanagement (the AI of your team is well above average in fact) but because there is a very tangible benefit to using the squad order system and instructing them to switch to sniper mode or hold a section of cover or whatever. Having said that, the order system does remain a tool. You are rarely forced to command your fellows and you can, if you're feeling light on your feet, play Commando as a more traditional shooter. Importantly, there are also some really bad command options presented so mechanically issuing orders doesn't work which avoids the danger of it becoming a simple "I win" option.
So the issuing of orders is a noticeably useful option given to the player. However it doesn't feel like a mechanic to be exploited because of the second great thing about its implementation - it is part of the game world. The obvious point there is that your character is the squad leader so you are expected to be telling everyone what to do. More subtly is the way the game encourages you to think carefully about your options. In any decent sized firefight there will be a dozen positions your squad can take up so you need to not only use the mechanic but think in real terms about the way this will benefit you. Most of the time it's fairly obvious stuff - but only if you're thinking about covering fire, line of sight and so on and then you're thinking about real world options rather than clicking buttons which helps with the immersion.
Something else important about the design of the squad is the commando skillset. Although each one of your team mates has a distinct personality, in terms of ability they are entirely interchangeable. While that may sound simplistic it helps avoid making everything too obvious. You don't drop your sniper in the sniper spot simply because he's a sniper, for example. You can have intersecting fields of sniper fire if you want - you aren't restricted to just one guy with a rifle. You also don't have the problem of needing to blow something up and your demo guy is the one who decided to get his face shot off - someone else can step up to the task.
Linked to this is the way you can define your own role in the team. You have the same skills as your team mates which means every time you order someone to set a bomb or hack a terminal, you can do it instead if you prefer. In the middle of a firefight, you can order one of your chaps to get on with hacking while you shoot the enemies off him, however if you prefer you can instead put yourself in danger and order your team to give you covering fire. It may not sound like much, but this really makes you feel like part of a team instead of above it which does wonders for the oh-so-important immersion.
There are other clever design ideas - regenerating shields but collectible health so you can barely survive a firefight and limp into the next bit without being completely crippled springs to mind - however the squad control system is what makes Commando interesting. It manages not only to avoid being a gimmick, but also demonstrate how a cleverly applied gameplay mechanic can enhance atmosphere and immersion.