Looking at turn-based and real-time strategy games, there are a lot of ideas that could make for really unique and interesting gameplay if they were elaborated on, and used as an integral part of the design rather than just a neat feature. Total Annihilation had a commander unit you started with. Through the capabilities of this single unit, you could build every unit and structure in the game. Not only that, this commander remained useful throughout the game. It was the fastest building unit, had the most offensive ability out of any unit in the game. It generated resources for you to spend just by being in play. Also, when it died, it blew up in a massive thermonuclear explosion. Later there was Warcraft 3 and its whole hero scheme. This game provided a unit that didn't have the power to single-handedly raise an army, but was more like a general, leading the armies that you did build to victory through the hero's powerful individual abilities. They could bring their armies back to life. They could turn invisible and lead a whole army past enemy forces without ever being noticed. Unfortunately, heroes didn't blow up when they died, but still. I like this idea of having a central unit that really represents the player; something to bring the player down to the battlefield, and not just be a disembodied hand flying overhead in the sky. This unit would be more of an avatar than simply the player's primary tool; but I'm not quite sure how to do that.

I loved the way TA completely integrated the Commander into gameplay. The fact that you could cloak him, airlift him, use his D-Gun to instakill units, and use him as a massive battery in the beginning (heck, even kidnap him, though it was a cheap strategy) really made him a memorable part of the game.

I think there are a bunch of different things you can do to make the player identify with a unit more closely. One, for instance, would be customization and upgrading. Another would be carrying over memorable effects from one battle to another (such as scars, a Commander with a blown off arm, or even unique weapons you've retrieved from defeating other special characters).

OTOH, you could go full out and make the avatar a super unit in a kind of Battlezone like RTS game. You'd really identify with the unit if you had to control some of his unique abilities. One problem I ALWAYS had with the Commander was that he was so valuable I didn't want to leave him, and he could do little tactical thinking on his own. So either I got consummed with using him in some strategy, barely having time for everything else, or I kept him back at base. So a mix would have to tone down one element or another, or create mechanisms for switching (like phased movement, where you have some excuse to move units, then the avatar... you could be controlling a vampire that can only attack at night, for instance, or simply have a "hero phase / army phase")

Have you played Sacrifice? It's a sort of hybrid between third person action and strategy. Your avatar directs his troops from on the battle field (in third person mode); you use the mouse to control troops (which you summon via spells), and the keyboard to move your avatar. Your avatar has to run around the map in order to see what you are doing, so you have to lead an assault from the frontlines. I quite liked the game, it reminded me of Magic Carpet (one of my most favourite games).

An Avatar is central to the gameplay of Dominions 2, which is one of the best fantasy turn-based strategy games out there. In a lesser way, the same is true of Age of Wonders.

One of the downsides of having an important avatar is that the game can be centred around them sometimes to the detriment of strategy. Like in TA if commander death ended game, the commander would frequently be the target of nasty airstrikes. And if commander death didn't end game, then the commander unit effectively turned into a basic tactical nuke.

Of course, it wasn't really too bad in TA, because the game was well-balanced. But it can easily get out of hand, eg. TA:Kingdoms.